Starting phenix.real_space_refine on Thu Feb 22 23:32:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr3_34044/02_2024/7yr3_34044.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr3_34044/02_2024/7yr3_34044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr3_34044/02_2024/7yr3_34044.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr3_34044/02_2024/7yr3_34044.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr3_34044/02_2024/7yr3_34044.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr3_34044/02_2024/7yr3_34044.pdb" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 S 167 5.16 5 Cl 2 4.86 5 C 22772 2.51 5 N 5862 2.21 5 O 7094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 238": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 780": "OE1" <-> "OE2" Residue "B PHE 823": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 917": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1031": "OE1" <-> "OE2" Residue "B ASP 1041": "OD1" <-> "OD2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1092": "OE1" <-> "OE2" Residue "C ASP 53": "OD1" <-> "OD2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 578": "OD1" <-> "OD2" Residue "C TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C GLU 725": "OE1" <-> "OE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 543": "OD1" <-> "OD2" Residue "F PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 554": "OE1" <-> "OE2" Residue "F ASP 571": "OD1" <-> "OD2" Residue "F ASP 745": "OD1" <-> "OD2" Residue "F PHE 1109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 587": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 615": "OD1" <-> "OD2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 35899 Number of models: 1 Model: "" Number of chains: 21 Chain: "B" Number of atoms: 8258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1058, 8258 Classifications: {'peptide': 1058} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 56, 'TRANS': 1001} Chain breaks: 3 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "C" Number of atoms: 8426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1080, 8426 Classifications: {'peptide': 1080} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 58, 'TRANS': 1021} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "F" Number of atoms: 8335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1068, 8335 Classifications: {'peptide': 1068} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 57, 'TRANS': 1010} Chain breaks: 3 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "G" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4870 Classifications: {'peptide': 597} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 210 Unusual residues: {'NAG': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 15 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "F" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 182 Unusual residues: {'NAG': 13} Classifications: {'undetermined': 13} Link IDs: {None: 12} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 13 Chain: "G" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Chain: "G" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 71 Classifications: {'water': 71} Link IDs: {None: 70} Time building chain proxies: 17.85, per 1000 atoms: 0.50 Number of scatterers: 35899 At special positions: 0 Unit cell: (152.88, 163.28, 243.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 Cl 2 17.00 S 167 16.00 O 7094 8.00 N 5862 7.00 C 22772 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.05 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 131 " - pdb=" SG CYS F 166 " distance=2.03 Simple disulfide: pdb=" SG CYS F 291 " - pdb=" SG CYS F 301 " distance=2.03 Simple disulfide: pdb=" SG CYS F 336 " - pdb=" SG CYS F 361 " distance=2.02 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.04 Simple disulfide: pdb=" SG CYS F 391 " - pdb=" SG CYS F 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS F 617 " - pdb=" SG CYS F 649 " distance=2.03 Simple disulfide: pdb=" SG CYS F 662 " - pdb=" SG CYS F 671 " distance=2.03 Simple disulfide: pdb=" SG CYS F 738 " - pdb=" SG CYS F 760 " distance=2.03 Simple disulfide: pdb=" SG CYS F 743 " - pdb=" SG CYS F 749 " distance=2.03 Simple disulfide: pdb=" SG CYS F1032 " - pdb=" SG CYS F1043 " distance=2.03 Simple disulfide: pdb=" SG CYS F1082 " - pdb=" SG CYS F1126 " distance=2.03 Simple disulfide: pdb=" SG CYS G 133 " - pdb=" SG CYS G 141 " distance=2.03 Simple disulfide: pdb=" SG CYS G 344 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 530 " - pdb=" SG CYS G 542 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG E 1 " - " NAG E 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG B1310 " - " ASN B 603 " " NAG B1311 " - " ASN B 616 " " NAG B1312 " - " ASN B 657 " " NAG B1313 " - " ASN B 709 " " NAG C1310 " - " ASN C 603 " " NAG C1311 " - " ASN C 616 " " NAG C1312 " - " ASN C 657 " " NAG C1313 " - " ASN C 709 " " NAG C1315 " - " ASN C1134 " " NAG D 903 " - " ASN D 546 " " NAG D 904 " - " ASN D 90 " " NAG D 905 " - " ASN D 322 " " NAG D 906 " - " ASN D 53 " " NAG F1309 " - " ASN F 616 " " NAG F1311 " - " ASN F 709 " " NAG F1313 " - " ASN F1134 " " NAG G 903 " - " ASN G 546 " " NAG G 904 " - " ASN G 90 " " NAG G 905 " - " ASN G 322 " " NAG G 906 " - " ASN G 53 " " NAG H 1 " - " ASN B1074 " " NAG I 1 " - " ASN C 717 " " NAG K 1 " - " ASN C1074 " " NAG N 1 " - " ASN F1074 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.43 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 901 " pdb="ZN ZN D 901 " - pdb=" ND1 HIS D 378 " pdb="ZN ZN D 901 " - pdb=" NE2 HIS D 374 " pdb=" ZN G 901 " pdb="ZN ZN G 901 " - pdb=" NE2 HIS G 374 " pdb="ZN ZN G 901 " - pdb=" NE2 HIS G 378 " 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8262 Finding SS restraints... Secondary structure from input PDB file: 114 helices and 57 sheets defined 34.6% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.33 Creating SS restraints... Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.630A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 372 removed outlier: 4.070A pdb=" N PHE B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA B 372 " --> pdb=" O TYR B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 372' Processing helix chain 'B' and resid 384 through 388 removed outlier: 3.644A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 384 through 388' Processing helix chain 'B' and resid 403 through 410 removed outlier: 4.341A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 737 through 742 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.537A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 783 removed outlier: 3.567A pdb=" N ARG B 765 " --> pdb=" O THR B 761 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 869 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 removed outlier: 3.861A pdb=" N ALA B 903 " --> pdb=" O PRO B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.798A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.792A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN B1002 " --> pdb=" O THR B 998 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 244 through 247 removed outlier: 3.621A pdb=" N SER C 247 " --> pdb=" O LEU C 244 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 244 through 247' Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.878A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 756 removed outlier: 3.701A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 760 through 783 removed outlier: 3.837A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.596A pdb=" N ALA C 871 " --> pdb=" O ASP C 867 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLN C 872 " --> pdb=" O GLU C 868 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.709A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 removed outlier: 4.150A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU C 918 " --> pdb=" O ASN C 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 913 through 918' Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.906A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR C 941 " --> pdb=" O SER C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 976 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.668A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 53 removed outlier: 4.049A pdb=" N GLN D 24 " --> pdb=" O THR D 20 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 82 removed outlier: 4.212A pdb=" N MET D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 146 through 155 Processing helix chain 'D' and resid 157 through 172 removed outlier: 4.077A pdb=" N VAL D 172 " --> pdb=" O TRP D 168 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 194 Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 218 through 252 removed outlier: 3.666A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 319 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.915A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.968A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 Processing helix chain 'D' and resid 400 through 414 Processing helix chain 'D' and resid 414 through 421 removed outlier: 3.801A pdb=" N ILE D 421 " --> pdb=" O HIS D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 removed outlier: 4.454A pdb=" N GLN D 429 " --> pdb=" O PRO D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 446 Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 481 removed outlier: 4.598A pdb=" N GLU D 479 " --> pdb=" O LYS D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 removed outlier: 3.510A pdb=" N SER D 507 " --> pdb=" O LEU D 503 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 533 Processing helix chain 'D' and resid 538 through 542 Processing helix chain 'D' and resid 547 through 561 removed outlier: 3.844A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU D 560 " --> pdb=" O ASN D 556 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY D 561 " --> pdb=" O MET D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.636A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 599 Proline residue: D 590 - end of helix Processing helix chain 'D' and resid 600 through 602 No H-bonds generated for 'chain 'D' and resid 600 through 602' Processing helix chain 'F' and resid 294 through 303 Processing helix chain 'F' and resid 338 through 343 Processing helix chain 'F' and resid 367 through 372 removed outlier: 3.972A pdb=" N ASN F 370 " --> pdb=" O VAL F 367 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ALA F 372 " --> pdb=" O TYR F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 405 through 408 removed outlier: 3.705A pdb=" N SER F 408 " --> pdb=" O ASN F 405 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 405 through 408' Processing helix chain 'F' and resid 417 through 422 Processing helix chain 'F' and resid 737 through 743 removed outlier: 3.574A pdb=" N TYR F 741 " --> pdb=" O ASP F 737 " (cutoff:3.500A) Processing helix chain 'F' and resid 746 through 755 removed outlier: 3.639A pdb=" N GLN F 755 " --> pdb=" O ASN F 751 " (cutoff:3.500A) Processing helix chain 'F' and resid 760 through 783 Processing helix chain 'F' and resid 816 through 826 Processing helix chain 'F' and resid 869 through 884 Processing helix chain 'F' and resid 886 through 891 removed outlier: 4.085A pdb=" N ALA F 890 " --> pdb=" O TRP F 886 " (cutoff:3.500A) Processing helix chain 'F' and resid 897 through 908 removed outlier: 3.516A pdb=" N TYR F 904 " --> pdb=" O MET F 900 " (cutoff:3.500A) Processing helix chain 'F' and resid 913 through 918 removed outlier: 4.295A pdb=" N TYR F 917 " --> pdb=" O GLN F 913 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU F 918 " --> pdb=" O ASN F 914 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 913 through 918' Processing helix chain 'F' and resid 919 through 941 removed outlier: 3.896A pdb=" N GLN F 935 " --> pdb=" O ILE F 931 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASP F 936 " --> pdb=" O GLY F 932 " (cutoff:3.500A) Processing helix chain 'F' and resid 945 through 965 Processing helix chain 'F' and resid 976 through 984 Processing helix chain 'F' and resid 985 through 1033 removed outlier: 3.583A pdb=" N GLU F 990 " --> pdb=" O PRO F 986 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL F 991 " --> pdb=" O PRO F 987 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN F 992 " --> pdb=" O GLU F 988 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG F 995 " --> pdb=" O VAL F 991 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 52 removed outlier: 3.550A pdb=" N GLN G 24 " --> pdb=" O THR G 20 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP G 38 " --> pdb=" O HIS G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 83 Processing helix chain 'G' and resid 92 through 101 removed outlier: 3.585A pdb=" N GLN G 96 " --> pdb=" O THR G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 129 Processing helix chain 'G' and resid 146 through 155 Processing helix chain 'G' and resid 157 through 194 removed outlier: 3.613A pdb=" N VAL G 172 " --> pdb=" O TRP G 168 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLN G 175 " --> pdb=" O GLU G 171 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU G 176 " --> pdb=" O VAL G 172 " (cutoff:3.500A) Proline residue: G 178 - end of helix Processing helix chain 'G' and resid 198 through 206 Processing helix chain 'G' and resid 218 through 252 removed outlier: 3.504A pdb=" N ILE G 223 " --> pdb=" O ARG G 219 " (cutoff:3.500A) Proline residue: G 235 - end of helix Processing helix chain 'G' and resid 253 through 256 removed outlier: 4.155A pdb=" N ILE G 256 " --> pdb=" O PRO G 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 253 through 256' Processing helix chain 'G' and resid 275 through 277 No H-bonds generated for 'chain 'G' and resid 275 through 277' Processing helix chain 'G' and resid 278 through 283 Processing helix chain 'G' and resid 293 through 301 Processing helix chain 'G' and resid 303 through 317 Processing helix chain 'G' and resid 324 through 331 removed outlier: 4.069A pdb=" N TRP G 328 " --> pdb=" O THR G 324 " (cutoff:3.500A) Processing helix chain 'G' and resid 365 through 385 removed outlier: 3.546A pdb=" N TYR G 385 " --> pdb=" O TYR G 381 " (cutoff:3.500A) Processing helix chain 'G' and resid 389 through 393 Processing helix chain 'G' and resid 400 through 414 removed outlier: 3.585A pdb=" N THR G 414 " --> pdb=" O LEU G 410 " (cutoff:3.500A) Processing helix chain 'G' and resid 414 through 421 Processing helix chain 'G' and resid 425 through 429 removed outlier: 4.518A pdb=" N GLN G 429 " --> pdb=" O PRO G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 431 through 465 removed outlier: 3.695A pdb=" N GLU G 435 " --> pdb=" O ASP G 431 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLY G 448 " --> pdb=" O LEU G 444 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR G 449 " --> pdb=" O THR G 445 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU G 450 " --> pdb=" O ILE G 446 " (cutoff:3.500A) Proline residue: G 451 - end of helix Processing helix chain 'G' and resid 469 through 471 No H-bonds generated for 'chain 'G' and resid 469 through 471' Processing helix chain 'G' and resid 472 through 484 removed outlier: 3.529A pdb=" N LYS G 476 " --> pdb=" O GLN G 472 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N GLU G 479 " --> pdb=" O LYS G 475 " (cutoff:3.500A) Processing helix chain 'G' and resid 498 through 502 Processing helix chain 'G' and resid 503 through 508 Processing helix chain 'G' and resid 513 through 533 Processing helix chain 'G' and resid 538 through 542 removed outlier: 3.616A pdb=" N LYS G 541 " --> pdb=" O PRO G 538 " (cutoff:3.500A) Processing helix chain 'G' and resid 547 through 561 removed outlier: 3.609A pdb=" N MET G 557 " --> pdb=" O LYS G 553 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU G 560 " --> pdb=" O ASN G 556 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY G 561 " --> pdb=" O MET G 557 " (cutoff:3.500A) Processing helix chain 'G' and resid 565 through 575 removed outlier: 4.005A pdb=" N VAL G 573 " --> pdb=" O ALA G 569 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 600 Proline residue: G 590 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 27 through 30 Processing sheet with id=AA2, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.257A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AA4, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.743A pdb=" N HIS B 49 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.615A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY B 107 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 204 through 208 removed outlier: 3.630A pdb=" N TYR B 204 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS B 206 " --> pdb=" O GLU B 191 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 311 through 319 removed outlier: 3.793A pdb=" N GLY B 311 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR B 599 " --> pdb=" O GLY B 311 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR B 315 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.738A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP B 398 " --> pdb=" O VAL B 512 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 452 through 454 removed outlier: 4.086A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 538 through 541 Processing sheet with id=AB2, first strand: chain 'B' and resid 654 through 660 removed outlier: 4.725A pdb=" N THR B 696 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASN B 658 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ILE B 664 " --> pdb=" O ALA B 672 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'B' and resid 711 through 713 Processing sheet with id=AB5, first strand: chain 'B' and resid 717 through 722 Processing sheet with id=AB6, first strand: chain 'B' and resid 717 through 722 removed outlier: 3.700A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AB8, first strand: chain 'C' and resid 26 through 30 Processing sheet with id=AB9, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.061A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'C' and resid 50 through 55 removed outlier: 3.946A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.595A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 205 through 208 removed outlier: 3.547A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU C 191 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 311 through 319 removed outlier: 3.731A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 324 through 326 removed outlier: 7.090A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 324 through 326 removed outlier: 7.090A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.262A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.355A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 453 through 454 removed outlier: 4.311A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'C' and resid 655 through 656 removed outlier: 4.356A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.545A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.545A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 735 through 736 Processing sheet with id=AD6, first strand: chain 'C' and resid 1081 through 1082 Processing sheet with id=AD7, first strand: chain 'C' and resid 1089 through 1090 Processing sheet with id=AD8, first strand: chain 'D' and resid 132 through 133 Processing sheet with id=AD9, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.024A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.091A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 26 through 30 Processing sheet with id=AE3, first strand: chain 'F' and resid 36 through 37 removed outlier: 6.808A pdb=" N VAL F 36 " --> pdb=" O LEU F 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'F' and resid 50 through 55 removed outlier: 3.622A pdb=" N ASP F 287 " --> pdb=" O LYS F 278 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 84 through 85 removed outlier: 3.826A pdb=" N PHE F 106 " --> pdb=" O LEU F 117 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 205 through 208 removed outlier: 3.514A pdb=" N LYS F 206 " --> pdb=" O GLU F 191 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU F 191 " --> pdb=" O LYS F 206 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA F 93 " --> pdb=" O TYR F 266 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'F' and resid 311 through 313 removed outlier: 4.311A pdb=" N TYR F 612 " --> pdb=" O CYS F 649 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 354 through 355 removed outlier: 3.597A pdb=" N ASN F 354 " --> pdb=" O SER F 399 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 452 through 454 removed outlier: 3.821A pdb=" N TYR F 453 " --> pdb=" O GLN F 493 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'F' and resid 542 through 543 Processing sheet with id=AF3, first strand: chain 'F' and resid 551 through 554 Processing sheet with id=AF4, first strand: chain 'F' and resid 654 through 660 removed outlier: 5.336A pdb=" N GLU F 654 " --> pdb=" O ALA F 694 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N THR F 696 " --> pdb=" O GLU F 654 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N VAL F 656 " --> pdb=" O THR F 696 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER F 691 " --> pdb=" O GLN F 675 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN F 675 " --> pdb=" O SER F 691 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ILE F 670 " --> pdb=" O ILE F 666 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 711 through 715 Processing sheet with id=AF6, first strand: chain 'F' and resid 718 through 722 removed outlier: 7.008A pdb=" N VAL F1065 " --> pdb=" O LEU F1049 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 725 through 728 Processing sheet with id=AF8, first strand: chain 'F' and resid 733 through 735 removed outlier: 4.491A pdb=" N LYS F 733 " --> pdb=" O LEU F 861 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N SER F 735 " --> pdb=" O THR F 859 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 1081 through 1082 Processing sheet with id=AG1, first strand: chain 'G' and resid 132 through 133 Processing sheet with id=AG2, first strand: chain 'G' and resid 262 through 263 removed outlier: 5.932A pdb=" N LEU G 262 " --> pdb=" O VAL G 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG2 Processing sheet with id=AG3, first strand: chain 'G' and resid 347 through 352 removed outlier: 6.156A pdb=" N ASP G 355 " --> pdb=" O LEU G 351 " (cutoff:3.500A) 1343 hydrogen bonds defined for protein. 3765 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: 13.87 Time building geometry restraints manager: 14.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 11390 1.35 - 1.47: 9320 1.47 - 1.59: 15682 1.59 - 1.72: 0 1.72 - 1.84: 236 Bond restraints: 36628 Sorted by residual: bond pdb=" C1 NAG N 1 " pdb=" O5 NAG N 1 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C1 NAG K 1 " pdb=" O5 NAG K 1 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.44e+01 bond pdb=" N ILE F 332 " pdb=" CA ILE F 332 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.27e+00 bond pdb=" N ASN F 331 " pdb=" CA ASN F 331 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.25e-02 6.40e+03 7.58e+00 bond pdb=" N ASN F 334 " pdb=" CA ASN F 334 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.41e+00 ... (remaining 36623 not shown) Histogram of bond angle deviations from ideal: 97.44 - 104.93: 674 104.93 - 112.43: 18762 112.43 - 119.92: 12995 119.92 - 127.42: 17027 127.42 - 134.91: 379 Bond angle restraints: 49837 Sorted by residual: angle pdb=" C ASN B1135 " pdb=" CA ASN B1135 " pdb=" CB ASN B1135 " ideal model delta sigma weight residual 115.79 109.59 6.20 1.19e+00 7.06e-01 2.71e+01 angle pdb=" C TYR F1138 " pdb=" N ASP F1139 " pdb=" CA ASP F1139 " ideal model delta sigma weight residual 120.97 134.91 -13.94 2.84e+00 1.24e-01 2.41e+01 angle pdb=" CA LEU F 335 " pdb=" C LEU F 335 " pdb=" O LEU F 335 " ideal model delta sigma weight residual 122.27 116.63 5.64 1.16e+00 7.43e-01 2.36e+01 angle pdb=" N PHE C 759 " pdb=" CA PHE C 759 " pdb=" C PHE C 759 " ideal model delta sigma weight residual 113.20 107.50 5.70 1.21e+00 6.83e-01 2.22e+01 angle pdb=" N MET D 123 " pdb=" CA MET D 123 " pdb=" CB MET D 123 " ideal model delta sigma weight residual 110.28 116.50 -6.22 1.55e+00 4.16e-01 1.61e+01 ... (remaining 49832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.58: 21464 25.58 - 51.17: 1057 51.17 - 76.75: 133 76.75 - 102.33: 33 102.33 - 127.92: 7 Dihedral angle restraints: 22694 sinusoidal: 9844 harmonic: 12850 Sorted by residual: dihedral pdb=" CB CYS B 662 " pdb=" SG CYS B 662 " pdb=" SG CYS B 671 " pdb=" CB CYS B 671 " ideal model delta sinusoidal sigma weight residual -86.00 -8.45 -77.55 1 1.00e+01 1.00e-02 7.53e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -10.44 -75.56 1 1.00e+01 1.00e-02 7.21e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 33.35 59.65 1 1.00e+01 1.00e-02 4.75e+01 ... (remaining 22691 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 5118 0.079 - 0.158: 542 0.158 - 0.236: 13 0.236 - 0.315: 2 0.315 - 0.394: 1 Chirality restraints: 5676 Sorted by residual: chirality pdb=" C1 NAG H 1 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG H 1 " pdb=" O5 NAG H 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" CB ILE B 664 " pdb=" CA ILE B 664 " pdb=" CG1 ILE B 664 " pdb=" CG2 ILE B 664 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CB ILE B 197 " pdb=" CA ILE B 197 " pdb=" CG1 ILE B 197 " pdb=" CG2 ILE B 197 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 5673 not shown) Planarity restraints: 6396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU C 754 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C LEU C 754 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU C 754 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN C 755 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS F 336 " -0.052 5.00e-02 4.00e+02 7.83e-02 9.80e+00 pdb=" N PRO F 337 " 0.135 5.00e-02 4.00e+02 pdb=" CA PRO F 337 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 337 " -0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 349 " -0.010 2.00e-02 2.50e+03 1.52e-02 5.80e+00 pdb=" CG TRP D 349 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP D 349 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP D 349 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP D 349 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 349 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP D 349 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 349 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 349 " -0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP D 349 " -0.000 2.00e-02 2.50e+03 ... (remaining 6393 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 360 2.52 - 3.12: 27839 3.12 - 3.71: 55440 3.71 - 4.31: 75783 4.31 - 4.90: 125387 Nonbonded interactions: 284809 Sorted by model distance: nonbonded pdb=" CD2 HIS D 378 " pdb="ZN ZN D 901 " model vdw 1.930 1.960 nonbonded pdb=" OG SER C 605 " pdb=" OE1 GLN C 607 " model vdw 2.128 2.440 nonbonded pdb=" OG1 THR B 912 " pdb=" NE2 GLN B1106 " model vdw 2.153 2.520 nonbonded pdb=" OG SER D 607 " pdb=" OD1 ASP D 609 " model vdw 2.161 2.440 nonbonded pdb=" OE2 GLU G 398 " pdb=" O HOH G1001 " model vdw 2.161 2.440 ... (remaining 284804 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } ncs_group { reference = (chain 'B' and (resid 25 through 825 or resid 856 through 1144 or resid 1301 thr \ ough 1313)) selection = (chain 'C' and (resid 25 through 620 or resid 643 through 825 or resid 856 throu \ gh 1144 or resid 1301 through 1313)) selection = (chain 'F' and (resid 25 through 620 or resid 643 through 825 or resid 856 throu \ gh 1144 or resid 1301 through 1313)) } ncs_group { reference = chain 'D' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 8.830 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 95.160 Find NCS groups from input model: 2.710 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 36628 Z= 0.257 Angle : 0.628 13.940 49837 Z= 0.323 Chirality : 0.045 0.394 5676 Planarity : 0.004 0.078 6372 Dihedral : 14.552 127.918 14306 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.82 % Favored : 92.02 % Rotamer: Outliers : 0.13 % Allowed : 0.36 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.13), residues: 4374 helix: 1.25 (0.15), residues: 1336 sheet: -0.84 (0.20), residues: 652 loop : -1.65 (0.13), residues: 2386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D 349 HIS 0.013 0.001 HIS D 373 PHE 0.037 0.001 PHE D 369 TYR 0.033 0.001 TYR B 160 ARG 0.007 0.000 ARG F 237 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 275 time to evaluate : 3.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 453 TYR cc_start: 0.7960 (p90) cc_final: 0.7318 (p90) REVERT: D 360 MET cc_start: 0.0576 (tpt) cc_final: 0.0306 (tpp) REVERT: D 378 HIS cc_start: 0.2844 (t-90) cc_final: 0.2175 (t-90) REVERT: F 200 TYR cc_start: 0.6108 (m-80) cc_final: 0.5758 (m-80) REVERT: G 123 MET cc_start: 0.2180 (tpt) cc_final: 0.1253 (ptm) outliers start: 5 outliers final: 1 residues processed: 279 average time/residue: 0.4366 time to fit residues: 211.1942 Evaluate side-chains 209 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 208 time to evaluate : 3.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 335 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 369 optimal weight: 2.9990 chunk 331 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 113 optimal weight: 0.0970 chunk 223 optimal weight: 20.0000 chunk 176 optimal weight: 3.9990 chunk 342 optimal weight: 0.0870 chunk 132 optimal weight: 3.9990 chunk 208 optimal weight: 0.6980 chunk 254 optimal weight: 30.0000 chunk 396 optimal weight: 6.9990 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN B 282 ASN B 334 ASN ** B 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 601 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 36628 Z= 0.194 Angle : 0.580 9.427 49837 Z= 0.293 Chirality : 0.043 0.246 5676 Planarity : 0.004 0.087 6372 Dihedral : 8.596 103.299 6222 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.59 % Favored : 92.27 % Rotamer: Outliers : 0.49 % Allowed : 6.06 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % 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: -0.75 (0.13), residues: 4374 helix: 1.50 (0.14), residues: 1328 sheet: -0.63 (0.20), residues: 645 loop : -1.71 (0.13), residues: 2401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 353 HIS 0.012 0.001 HIS D 373 PHE 0.023 0.001 PHE D 369 TYR 0.027 0.001 TYR B 160 ARG 0.005 0.000 ARG F 237 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 241 time to evaluate : 3.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1002 GLN cc_start: 0.8313 (tm-30) cc_final: 0.8003 (tm-30) REVERT: C 453 TYR cc_start: 0.7945 (p90) cc_final: 0.7326 (p90) REVERT: C 955 ASN cc_start: 0.8386 (m-40) cc_final: 0.8003 (t0) REVERT: F 224 GLU cc_start: 0.7877 (pm20) cc_final: 0.7411 (pm20) REVERT: F 748 GLU cc_start: 0.7954 (pm20) cc_final: 0.7697 (pm20) REVERT: G 123 MET cc_start: 0.1941 (tpt) cc_final: 0.1113 (ptm) outliers start: 19 outliers final: 14 residues processed: 253 average time/residue: 0.4117 time to fit residues: 182.8779 Evaluate side-chains 226 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 212 time to evaluate : 3.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain C residue 409 GLN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 762 GLN Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 297 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 220 optimal weight: 1.9990 chunk 123 optimal weight: 0.0670 chunk 330 optimal weight: 5.9990 chunk 270 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 397 optimal weight: 20.0000 chunk 429 optimal weight: 5.9990 chunk 354 optimal weight: 3.9990 chunk 394 optimal weight: 7.9990 chunk 135 optimal weight: 1.9990 chunk 318 optimal weight: 20.0000 overall best weight: 2.2126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 378 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 544 ASN ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 36628 Z= 0.259 Angle : 0.582 10.503 49837 Z= 0.293 Chirality : 0.043 0.265 5676 Planarity : 0.004 0.091 6372 Dihedral : 7.893 103.604 6220 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.32 % Favored : 91.54 % Rotamer: Outliers : 1.04 % Allowed : 9.13 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.13), residues: 4374 helix: 1.53 (0.14), residues: 1325 sheet: -0.71 (0.20), residues: 655 loop : -1.74 (0.13), residues: 2394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 353 HIS 0.011 0.001 HIS G 34 PHE 0.018 0.001 PHE D 369 TYR 0.024 0.001 TYR B 160 ARG 0.004 0.000 ARG F 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 237 time to evaluate : 4.168 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 878 LEU cc_start: 0.8805 (tt) cc_final: 0.8450 (mp) REVERT: B 1002 GLN cc_start: 0.8346 (tm-30) cc_final: 0.8004 (tm-30) REVERT: C 453 TYR cc_start: 0.7977 (p90) cc_final: 0.7378 (p90) REVERT: D 67 ASP cc_start: 0.2273 (m-30) cc_final: 0.1937 (p0) REVERT: D 152 MET cc_start: -0.0515 (mmp) cc_final: -0.2056 (ttp) REVERT: D 376 MET cc_start: -0.0249 (tmm) cc_final: -0.0514 (tmm) REVERT: F 224 GLU cc_start: 0.7909 (pm20) cc_final: 0.7500 (pm20) REVERT: F 748 GLU cc_start: 0.8028 (pm20) cc_final: 0.7801 (pm20) outliers start: 40 outliers final: 21 residues processed: 263 average time/residue: 0.4130 time to fit residues: 189.8653 Evaluate side-chains 233 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 212 time to evaluate : 3.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 445 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 392 optimal weight: 0.9980 chunk 298 optimal weight: 6.9990 chunk 206 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 266 optimal weight: 7.9990 chunk 398 optimal weight: 10.0000 chunk 422 optimal weight: 10.0000 chunk 208 optimal weight: 0.6980 chunk 378 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 277 ASN ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 374 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 378 HIS ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 762 GLN ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 36628 Z= 0.204 Angle : 0.559 11.682 49837 Z= 0.280 Chirality : 0.043 0.264 5676 Planarity : 0.004 0.094 6372 Dihedral : 7.484 102.085 6220 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.18 % Favored : 91.68 % Rotamer: Outliers : 1.38 % Allowed : 10.48 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.13), residues: 4374 helix: 1.60 (0.14), residues: 1332 sheet: -0.74 (0.20), residues: 662 loop : -1.72 (0.13), residues: 2380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 48 HIS 0.011 0.001 HIS D 373 PHE 0.014 0.001 PHE B 201 TYR 0.023 0.001 TYR B 160 ARG 0.010 0.000 ARG F 214 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 227 time to evaluate : 3.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 759 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7841 (t80) REVERT: B 878 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8457 (mp) REVERT: B 1002 GLN cc_start: 0.8287 (tm-30) cc_final: 0.7996 (tm-30) REVERT: C 453 TYR cc_start: 0.7946 (p90) cc_final: 0.7368 (p90) REVERT: C 1095 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7538 (t80) REVERT: D 67 ASP cc_start: 0.2248 (m-30) cc_final: 0.1919 (p0) REVERT: D 333 LEU cc_start: -0.0208 (OUTLIER) cc_final: -0.0524 (pp) REVERT: F 214 ARG cc_start: 0.6613 (tpt170) cc_final: 0.6035 (tpt170) REVERT: F 224 GLU cc_start: 0.7883 (pm20) cc_final: 0.7473 (pm20) REVERT: G 175 GLN cc_start: 0.4173 (mp10) cc_final: 0.3739 (pp30) outliers start: 53 outliers final: 30 residues processed: 263 average time/residue: 0.4248 time to fit residues: 195.4077 Evaluate side-chains 245 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 211 time to evaluate : 3.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1095 PHE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 396 TYR Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 565 PHE Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 869 MET Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 360 MET Chi-restraints excluded: chain G residue 364 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 351 optimal weight: 1.9990 chunk 239 optimal weight: 6.9990 chunk 6 optimal weight: 0.0980 chunk 314 optimal weight: 10.0000 chunk 174 optimal weight: 0.9980 chunk 360 optimal weight: 0.5980 chunk 291 optimal weight: 0.0040 chunk 0 optimal weight: 10.0000 chunk 215 optimal weight: 20.0000 chunk 379 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 36628 Z= 0.144 Angle : 0.533 10.621 49837 Z= 0.266 Chirality : 0.042 0.355 5676 Planarity : 0.004 0.094 6372 Dihedral : 6.983 101.077 6220 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.22 % Favored : 92.66 % Rotamer: Outliers : 1.17 % Allowed : 11.86 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % 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: -0.57 (0.13), residues: 4374 helix: 1.78 (0.14), residues: 1331 sheet: -0.64 (0.20), residues: 662 loop : -1.65 (0.13), residues: 2381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 48 HIS 0.012 0.001 HIS D 373 PHE 0.016 0.001 PHE G 314 TYR 0.022 0.001 TYR B 160 ARG 0.003 0.000 ARG F 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 241 time to evaluate : 3.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 759 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7829 (t80) REVERT: B 878 LEU cc_start: 0.8699 (tt) cc_final: 0.8467 (mp) REVERT: B 983 ARG cc_start: 0.8257 (ttm110) cc_final: 0.8033 (ttm110) REVERT: C 453 TYR cc_start: 0.7950 (p90) cc_final: 0.7450 (p90) REVERT: C 955 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.7882 (t0) REVERT: C 1095 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7339 (t80) REVERT: D 67 ASP cc_start: 0.2266 (m-30) cc_final: 0.1938 (p0) REVERT: D 152 MET cc_start: -0.0631 (mmp) cc_final: -0.2042 (ttp) REVERT: D 333 LEU cc_start: -0.0328 (OUTLIER) cc_final: -0.0652 (pp) REVERT: F 224 GLU cc_start: 0.7773 (pm20) cc_final: 0.7370 (pm20) REVERT: F 856 ASN cc_start: 0.8910 (OUTLIER) cc_final: 0.8222 (p0) REVERT: G 175 GLN cc_start: 0.4293 (mp10) cc_final: 0.3888 (pp30) REVERT: G 376 MET cc_start: -0.2166 (ptm) cc_final: -0.2488 (ttp) outliers start: 45 outliers final: 27 residues processed: 275 average time/residue: 0.4298 time to fit residues: 205.6548 Evaluate side-chains 248 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 216 time to evaluate : 4.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 179 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 1095 PHE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 856 ASN Chi-restraints excluded: chain F residue 869 MET Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1122 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 360 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 142 optimal weight: 6.9990 chunk 380 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 chunk 248 optimal weight: 30.0000 chunk 104 optimal weight: 3.9990 chunk 422 optimal weight: 8.9990 chunk 350 optimal weight: 2.9990 chunk 195 optimal weight: 7.9990 chunk 35 optimal weight: 20.0000 chunk 139 optimal weight: 4.9990 chunk 221 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN B 148 ASN B 762 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 801 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 751 ASN ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.162 36628 Z= 0.480 Angle : 0.729 10.871 49837 Z= 0.367 Chirality : 0.047 0.304 5676 Planarity : 0.005 0.096 6372 Dihedral : 7.973 104.372 6220 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.11 % Favored : 89.73 % Rotamer: Outliers : 2.42 % Allowed : 13.22 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.12 (0.13), residues: 4374 helix: 1.29 (0.14), residues: 1306 sheet: -0.91 (0.21), residues: 649 loop : -1.94 (0.12), residues: 2419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 353 HIS 0.024 0.002 HIS F 69 PHE 0.021 0.002 PHE F 318 TYR 0.024 0.002 TYR B 160 ARG 0.026 0.001 ARG F 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 212 time to evaluate : 4.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 759 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.8128 (t80) REVERT: B 878 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8465 (tt) REVERT: B 983 ARG cc_start: 0.8326 (ttm110) cc_final: 0.8082 (ttm110) REVERT: C 342 PHE cc_start: 0.7651 (m-80) cc_final: 0.7268 (m-80) REVERT: C 396 TYR cc_start: 0.7076 (m-80) cc_final: 0.6447 (m-10) REVERT: C 1095 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8047 (t80) REVERT: D 67 ASP cc_start: 0.2282 (m-30) cc_final: 0.1932 (p0) REVERT: D 152 MET cc_start: -0.0490 (mmp) cc_final: -0.2034 (ttp) REVERT: D 333 LEU cc_start: -0.0710 (OUTLIER) cc_final: -0.1047 (pp) REVERT: F 177 MET cc_start: 0.7379 (ttt) cc_final: 0.6861 (mmp) REVERT: F 224 GLU cc_start: 0.8103 (pm20) cc_final: 0.7702 (pm20) REVERT: F 806 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8743 (mm) REVERT: F 856 ASN cc_start: 0.8959 (OUTLIER) cc_final: 0.8254 (p0) REVERT: G 175 GLN cc_start: 0.4438 (mp10) cc_final: 0.3910 (pp30) outliers start: 93 outliers final: 57 residues processed: 284 average time/residue: 0.4907 time to fit residues: 242.1174 Evaluate side-chains 256 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 193 time to evaluate : 4.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 266 TYR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 552 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1095 PHE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 533 LEU Chi-restraints excluded: chain F residue 565 PHE Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 595 VAL Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 747 THR Chi-restraints excluded: chain F residue 806 LEU Chi-restraints excluded: chain F residue 856 ASN Chi-restraints excluded: chain F residue 869 MET Chi-restraints excluded: chain F residue 911 VAL Chi-restraints excluded: chain F residue 934 ILE Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1122 VAL Chi-restraints excluded: chain F residue 1139 ASP Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 338 ASN Chi-restraints excluded: chain G residue 360 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 407 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 240 optimal weight: 3.9990 chunk 308 optimal weight: 0.9980 chunk 239 optimal weight: 10.0000 chunk 355 optimal weight: 0.9980 chunk 236 optimal weight: 30.0000 chunk 421 optimal weight: 20.0000 chunk 263 optimal weight: 20.0000 chunk 256 optimal weight: 0.9980 chunk 194 optimal weight: 0.2980 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 211 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1088 HIS ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 801 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 505 HIS F 544 ASN ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 36628 Z= 0.202 Angle : 0.579 9.686 49837 Z= 0.291 Chirality : 0.044 0.270 5676 Planarity : 0.004 0.098 6372 Dihedral : 7.364 102.385 6220 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.91 % Favored : 91.98 % Rotamer: Outliers : 1.93 % Allowed : 13.97 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.84 (0.13), residues: 4374 helix: 1.57 (0.14), residues: 1322 sheet: -0.76 (0.21), residues: 652 loop : -1.82 (0.13), residues: 2400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 48 HIS 0.014 0.001 HIS D 373 PHE 0.023 0.001 PHE B 201 TYR 0.020 0.001 TYR C1067 ARG 0.003 0.000 ARG C 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 225 time to evaluate : 3.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 759 PHE cc_start: 0.8319 (OUTLIER) cc_final: 0.8091 (t80) REVERT: B 878 LEU cc_start: 0.8728 (OUTLIER) cc_final: 0.8403 (mp) REVERT: B 983 ARG cc_start: 0.8302 (ttm110) cc_final: 0.8098 (ttm110) REVERT: C 342 PHE cc_start: 0.7568 (m-80) cc_final: 0.7295 (m-80) REVERT: C 453 TYR cc_start: 0.7903 (p90) cc_final: 0.7405 (p90) REVERT: C 955 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8058 (t0) REVERT: C 1095 PHE cc_start: 0.8343 (OUTLIER) cc_final: 0.7751 (t80) REVERT: D 67 ASP cc_start: 0.2290 (m-30) cc_final: 0.1946 (p0) REVERT: D 152 MET cc_start: -0.0617 (mmp) cc_final: -0.2123 (ttp) REVERT: D 333 LEU cc_start: -0.0851 (OUTLIER) cc_final: -0.1167 (pp) REVERT: F 177 MET cc_start: 0.7350 (ttt) cc_final: 0.6843 (mmp) REVERT: F 748 GLU cc_start: 0.8126 (pm20) cc_final: 0.7807 (pm20) REVERT: F 856 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8244 (p0) REVERT: G 175 GLN cc_start: 0.4442 (mp10) cc_final: 0.3909 (pp30) outliers start: 74 outliers final: 56 residues processed: 277 average time/residue: 0.4119 time to fit residues: 198.9406 Evaluate side-chains 269 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 207 time to evaluate : 3.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 402 ILE Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 737 ASP Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1095 PHE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain C residue 1122 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 565 PHE Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 598 ILE Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 737 ASP Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 761 THR Chi-restraints excluded: chain F residue 856 ASN Chi-restraints excluded: chain F residue 869 MET Chi-restraints excluded: chain F residue 911 VAL Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1122 VAL Chi-restraints excluded: chain F residue 1139 ASP Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 338 ASN Chi-restraints excluded: chain G residue 360 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 260 optimal weight: 0.0970 chunk 168 optimal weight: 3.9990 chunk 251 optimal weight: 30.0000 chunk 126 optimal weight: 8.9990 chunk 82 optimal weight: 0.4980 chunk 81 optimal weight: 2.9990 chunk 267 optimal weight: 30.0000 chunk 286 optimal weight: 7.9990 chunk 208 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 331 optimal weight: 0.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 36628 Z= 0.211 Angle : 0.577 9.771 49837 Z= 0.289 Chirality : 0.043 0.266 5676 Planarity : 0.004 0.099 6372 Dihedral : 7.174 102.353 6220 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.73 % Favored : 91.15 % Rotamer: Outliers : 2.00 % Allowed : 14.49 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % 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: -0.78 (0.13), residues: 4374 helix: 1.62 (0.14), residues: 1330 sheet: -0.75 (0.20), residues: 659 loop : -1.78 (0.13), residues: 2385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 48 HIS 0.014 0.001 HIS D 373 PHE 0.023 0.001 PHE B 565 TYR 0.024 0.001 TYR C 473 ARG 0.006 0.000 ARG G 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 222 time to evaluate : 3.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 759 PHE cc_start: 0.8288 (OUTLIER) cc_final: 0.8034 (t80) REVERT: B 878 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8400 (mp) REVERT: C 342 PHE cc_start: 0.7582 (m-80) cc_final: 0.7309 (m-80) REVERT: C 453 TYR cc_start: 0.7961 (p90) cc_final: 0.7425 (p90) REVERT: C 1095 PHE cc_start: 0.8348 (OUTLIER) cc_final: 0.7666 (t80) REVERT: D 67 ASP cc_start: 0.2289 (m-30) cc_final: 0.1953 (p0) REVERT: D 333 LEU cc_start: -0.0593 (OUTLIER) cc_final: -0.0876 (pp) REVERT: F 177 MET cc_start: 0.7319 (ttt) cc_final: 0.6852 (mmp) REVERT: F 224 GLU cc_start: 0.7929 (pm20) cc_final: 0.7513 (pm20) REVERT: F 748 GLU cc_start: 0.8155 (pm20) cc_final: 0.7873 (pm20) REVERT: F 856 ASN cc_start: 0.8880 (OUTLIER) cc_final: 0.8216 (p0) REVERT: G 123 MET cc_start: 0.1751 (tpt) cc_final: 0.0945 (tpt) REVERT: G 175 GLN cc_start: 0.4242 (mp10) cc_final: 0.3740 (pp30) outliers start: 77 outliers final: 57 residues processed: 278 average time/residue: 0.4292 time to fit residues: 208.8948 Evaluate side-chains 275 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 213 time to evaluate : 3.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1095 PHE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 565 PHE Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 598 ILE Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 856 ASN Chi-restraints excluded: chain F residue 869 MET Chi-restraints excluded: chain F residue 911 VAL Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1122 VAL Chi-restraints excluded: chain F residue 1139 ASP Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 338 ASN Chi-restraints excluded: chain G residue 360 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 383 optimal weight: 1.9990 chunk 403 optimal weight: 6.9990 chunk 368 optimal weight: 5.9990 chunk 392 optimal weight: 10.0000 chunk 236 optimal weight: 6.9990 chunk 170 optimal weight: 0.8980 chunk 308 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 354 optimal weight: 0.6980 chunk 371 optimal weight: 4.9990 chunk 391 optimal weight: 8.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 36628 Z= 0.285 Angle : 0.613 14.021 49837 Z= 0.306 Chirality : 0.044 0.271 5676 Planarity : 0.004 0.100 6372 Dihedral : 7.258 102.742 6220 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.98 % Favored : 90.90 % Rotamer: Outliers : 2.03 % Allowed : 14.83 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.86 (0.13), residues: 4374 helix: 1.52 (0.14), residues: 1330 sheet: -0.80 (0.20), residues: 677 loop : -1.82 (0.13), residues: 2367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 48 HIS 0.014 0.001 HIS D 373 PHE 0.021 0.001 PHE B 201 TYR 0.021 0.001 TYR B 160 ARG 0.004 0.000 ARG F 357 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 212 time to evaluate : 3.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 759 PHE cc_start: 0.8309 (OUTLIER) cc_final: 0.8108 (t80) REVERT: B 878 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8348 (tt) REVERT: C 342 PHE cc_start: 0.7562 (m-80) cc_final: 0.7288 (m-80) REVERT: C 453 TYR cc_start: 0.7953 (p90) cc_final: 0.7431 (p90) REVERT: C 1095 PHE cc_start: 0.8421 (OUTLIER) cc_final: 0.7756 (t80) REVERT: D 67 ASP cc_start: 0.2292 (m-30) cc_final: 0.1946 (p0) REVERT: D 333 LEU cc_start: -0.0754 (OUTLIER) cc_final: -0.0985 (pp) REVERT: F 177 MET cc_start: 0.7272 (ttt) cc_final: 0.6822 (mmp) REVERT: F 224 GLU cc_start: 0.7928 (pm20) cc_final: 0.7500 (pm20) REVERT: F 748 GLU cc_start: 0.8191 (pm20) cc_final: 0.7952 (pm20) REVERT: F 806 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8707 (mm) REVERT: F 856 ASN cc_start: 0.8882 (OUTLIER) cc_final: 0.8218 (p0) REVERT: G 102 GLN cc_start: 0.1214 (mm-40) cc_final: 0.0675 (tt0) REVERT: G 123 MET cc_start: 0.1760 (tpt) cc_final: 0.0982 (tpt) REVERT: G 175 GLN cc_start: 0.4411 (mp10) cc_final: 0.3905 (pp30) REVERT: G 400 PHE cc_start: -0.0701 (m-10) cc_final: -0.0902 (m-10) outliers start: 78 outliers final: 61 residues processed: 268 average time/residue: 0.4267 time to fit residues: 198.2129 Evaluate side-chains 276 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 209 time to evaluate : 4.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 759 PHE Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 394 ASN Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 697 MET Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1095 PHE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 565 PHE Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 598 ILE Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 737 ASP Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 806 LEU Chi-restraints excluded: chain F residue 856 ASN Chi-restraints excluded: chain F residue 869 MET Chi-restraints excluded: chain F residue 911 VAL Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1122 VAL Chi-restraints excluded: chain F residue 1139 ASP Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 82 MET Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 338 ASN Chi-restraints excluded: chain G residue 360 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 257 optimal weight: 8.9990 chunk 415 optimal weight: 30.0000 chunk 253 optimal weight: 3.9990 chunk 196 optimal weight: 0.8980 chunk 288 optimal weight: 10.0000 chunk 435 optimal weight: 5.9990 chunk 400 optimal weight: 20.0000 chunk 346 optimal weight: 0.7980 chunk 35 optimal weight: 20.0000 chunk 267 optimal weight: 20.0000 chunk 212 optimal weight: 5.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** B1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 148 ASN ** C 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.134 36628 Z= 0.373 Angle : 0.665 13.168 49837 Z= 0.333 Chirality : 0.045 0.296 5676 Planarity : 0.004 0.101 6372 Dihedral : 7.536 103.623 6220 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.92 % Favored : 89.96 % Rotamer: Outliers : 1.82 % Allowed : 14.98 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.05 (0.13), residues: 4374 helix: 1.38 (0.14), residues: 1321 sheet: -0.85 (0.20), residues: 670 loop : -1.96 (0.13), residues: 2383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 48 HIS 0.015 0.001 HIS D 373 PHE 0.023 0.002 PHE C1095 TYR 0.025 0.002 TYR C 396 ARG 0.007 0.001 ARG G 514 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8748 Ramachandran restraints generated. 4374 Oldfield, 0 Emsley, 4374 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 204 time to evaluate : 3.841 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: B 878 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8412 (tt) REVERT: C 342 PHE cc_start: 0.7586 (m-80) cc_final: 0.7248 (m-80) REVERT: C 392 PHE cc_start: 0.8071 (m-10) cc_final: 0.7766 (m-10) REVERT: C 1095 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.7878 (t80) REVERT: D 67 ASP cc_start: 0.2315 (m-30) cc_final: 0.1966 (p0) REVERT: D 333 LEU cc_start: -0.0802 (OUTLIER) cc_final: -0.1038 (pp) REVERT: F 177 MET cc_start: 0.7300 (ttt) cc_final: 0.6819 (mmp) REVERT: F 224 GLU cc_start: 0.7975 (pm20) cc_final: 0.7542 (pm20) REVERT: F 806 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8774 (mm) REVERT: F 856 ASN cc_start: 0.8894 (OUTLIER) cc_final: 0.8257 (p0) REVERT: G 123 MET cc_start: 0.1877 (tpt) cc_final: 0.1145 (tpt) REVERT: G 175 GLN cc_start: 0.4196 (mp10) cc_final: 0.3822 (pp30) outliers start: 70 outliers final: 58 residues processed: 254 average time/residue: 0.4410 time to fit residues: 194.8385 Evaluate side-chains 261 residues out of total 3860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 198 time to evaluate : 3.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 41 LYS Chi-restraints excluded: chain B residue 42 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 294 ASP Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 595 VAL Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 786 LYS Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 1129 VAL Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 511 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 955 ASN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1095 PHE Chi-restraints excluded: chain C residue 1096 VAL Chi-restraints excluded: chain D residue 134 ASN Chi-restraints excluded: chain D residue 142 LEU Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 333 LEU Chi-restraints excluded: chain D residue 573 VAL Chi-restraints excluded: chain F residue 33 THR Chi-restraints excluded: chain F residue 62 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 510 VAL Chi-restraints excluded: chain F residue 512 VAL Chi-restraints excluded: chain F residue 518 LEU Chi-restraints excluded: chain F residue 531 THR Chi-restraints excluded: chain F residue 565 PHE Chi-restraints excluded: chain F residue 569 ILE Chi-restraints excluded: chain F residue 598 ILE Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 737 ASP Chi-restraints excluded: chain F residue 740 MET Chi-restraints excluded: chain F residue 806 LEU Chi-restraints excluded: chain F residue 856 ASN Chi-restraints excluded: chain F residue 867 ASP Chi-restraints excluded: chain F residue 869 MET Chi-restraints excluded: chain F residue 911 VAL Chi-restraints excluded: chain F residue 979 ASP Chi-restraints excluded: chain F residue 1104 VAL Chi-restraints excluded: chain F residue 1122 VAL Chi-restraints excluded: chain F residue 1139 ASP Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 297 MET Chi-restraints excluded: chain G residue 338 ASN Chi-restraints excluded: chain G residue 360 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 437 random chunks: chunk 275 optimal weight: 5.9990 chunk 369 optimal weight: 0.6980 chunk 106 optimal weight: 0.0270 chunk 319 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 96 optimal weight: 0.8980 chunk 347 optimal weight: 0.0270 chunk 145 optimal weight: 1.9990 chunk 356 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 overall best weight: 0.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 ASN B 196 ASN ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1011 GLN ** C 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1011 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 552 GLN ** G 578 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.187951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.122127 restraints weight = 79728.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.124054 restraints weight = 36092.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.125660 restraints weight = 21974.136| |-----------------------------------------------------------------------------| r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 36628 Z= 0.160 Angle : 0.581 12.445 49837 Z= 0.290 Chirality : 0.043 0.301 5676 Planarity : 0.004 0.101 6372 Dihedral : 6.978 101.241 6220 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.43 % Favored : 92.46 % Rotamer: Outliers : 1.48 % Allowed : 15.63 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.89 % 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: -0.77 (0.13), residues: 4374 helix: 1.62 (0.15), residues: 1327 sheet: -0.72 (0.20), residues: 674 loop : -1.78 (0.13), residues: 2373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP D 48 HIS 0.013 0.001 HIS D 373 PHE 0.027 0.001 PHE B 565 TYR 0.020 0.001 TYR C1067 ARG 0.004 0.000 ARG G 514 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6684.22 seconds wall clock time: 123 minutes 57.18 seconds (7437.18 seconds total)