Starting phenix.real_space_refine on Sat Aug 10 22:55:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwi_32866/08_2024/7wwi_32866.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwi_32866/08_2024/7wwi_32866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwi_32866/08_2024/7wwi_32866.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwi_32866/08_2024/7wwi_32866.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwi_32866/08_2024/7wwi_32866.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwi_32866/08_2024/7wwi_32866.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.039 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 19271 2.51 5 N 4986 2.21 5 O 5848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 654": "OE1" <-> "OE2" Residue "A ASP 994": "OD1" <-> "OD2" Residue "A GLU 1031": "OE1" <-> "OE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B GLU 554": "OE1" <-> "OE2" Residue "B TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 988": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "C GLU 773": "OE1" <-> "OE2" Residue "C GLU 780": "OE1" <-> "OE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I GLU 46": "OE1" <-> "OE2" Residue "I GLU 82": "OE1" <-> "OE2" Residue "I GLU 89": "OE1" <-> "OE2" Residue "I GLU 101": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 30237 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 8121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8121 Classifications: {'peptide': 1034} Link IDs: {'PTRANS': 57, 'TRANS': 976} Chain breaks: 8 Chain: "B" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8126 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Chain: "C" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1035, 8126 Classifications: {'peptide': 1035} Link IDs: {'PTRANS': 57, 'TRANS': 977} Chain breaks: 8 Chain: "D" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "E" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "F" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 828 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "H" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 102} Chain: "I" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 922 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 9.84, per 1000 atoms: 0.33 Number of scatterers: 30237 At special positions: 0 Unit cell: (145.14, 156.62, 222.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 5848 8.00 N 4986 7.00 C 19271 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 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=2.04 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 709 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 709 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 234 " " NAG C1303 " - " ASN C 282 " " NAG C1304 " - " ASN C 331 " " NAG C1305 " - " ASN C 709 " " NAG J 1 " - " ASN C 801 " " NAG K 1 " - " ASN C1074 " " NAG L 1 " - " ASN C1098 " " NAG M 1 " - " ASN C1134 " " NAG N 1 " - " ASN B 717 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN B 801 " " NAG Q 1 " - " ASN B1074 " " NAG R 1 " - " ASN B1098 " " NAG S 1 " - " ASN B1134 " " NAG T 1 " - " ASN A 717 " " NAG U 1 " - " ASN A 801 " " NAG V 1 " - " ASN A1098 " " NAG W 1 " - " ASN A1134 " Time building additional restraints: 13.45 Conformation dependent library (CDL) restraints added in 6.0 seconds 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7084 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 59 sheets defined 21.1% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.05 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 366 through 371 Processing helix chain 'A' and resid 383 through 387 removed outlier: 3.514A pdb=" N LYS A 386 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.259A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.583A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 755 removed outlier: 4.045A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 891 removed outlier: 4.117A pdb=" N GLY A 891 " --> pdb=" O PHE A 888 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 941 removed outlier: 4.423A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LYS A 921 " --> pdb=" O TYR A 917 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N LEU A 922 " --> pdb=" O GLU A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.833A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.056A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.154A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.779A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N LEU B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.387A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 422 Processing helix chain 'B' and resid 737 through 743 removed outlier: 3.548A pdb=" N CYS B 743 " --> pdb=" O THR B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 746 through 754 removed outlier: 3.705A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.550A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.575A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.188A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 942 through 944 No H-bonds generated for 'chain 'B' and resid 942 through 944' Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.691A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.472A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1147 removed outlier: 3.862A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 3.887A pdb=" N LEU C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.064A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.657A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.812A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.146A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 966 removed outlier: 3.714A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU C 966 " --> pdb=" O LEU C 962 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.046A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1147 Processing helix chain 'D' and resid 79 through 83 Processing helix chain 'E' and resid 28 through 30 No H-bonds generated for 'chain 'E' and resid 28 through 30' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.897A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.795A pdb=" N PHE F 83 " --> pdb=" O PRO F 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 65 removed outlier: 4.090A pdb=" N GLN G 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 62 through 65' Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.623A pdb=" N THR G 91 " --> pdb=" O SER G 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 83 removed outlier: 3.949A pdb=" N PHE H 83 " --> pdb=" O PRO H 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 65 Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.533A pdb=" N THR I 91 " --> pdb=" O SER I 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.465A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.374A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.801A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.588A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 142 removed outlier: 8.302A pdb=" N CYS A 136 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 10.358A pdb=" N SER A 162 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 10.371A pdb=" N ASP A 138 " --> pdb=" O TYR A 160 " (cutoff:3.500A) removed outlier: 7.871A pdb=" N TYR A 160 " --> pdb=" O ASP A 138 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 7.328A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.247A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.896A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.082A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.604A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.946A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 734 through 735 Processing sheet with id=AB6, first strand: chain 'A' and resid 787 through 790 removed outlier: 3.710A pdb=" N LYS A 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB8, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id=AB9, first strand: chain 'B' and resid 27 through 30 removed outlier: 8.223A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 42 through 43 Processing sheet with id=AC2, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.055A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 5.987A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASN B 165 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLN B 134 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA B 163 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N CYS B 136 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N SER B 161 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N ASP B 138 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N VAL B 159 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N PHE B 140 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N PHE B 157 " --> pdb=" O PHE B 140 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.485A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 356 through 358 Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.101A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.709A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.514A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AD3, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD4, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD5, first strand: chain 'C' and resid 27 through 30 removed outlier: 8.001A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.767A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.732A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.892A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.508A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL C 126 " --> pdb=" O VAL C 171 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL C 171 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N ILE C 128 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLU C 169 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 7.939A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) removed outlier: 8.970A pdb=" N CYS C 136 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N SER C 161 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ASP C 138 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N VAL C 159 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE C 140 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N PHE C 157 " --> pdb=" O PHE C 140 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.390A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 325 through 328 Processing sheet with id=AE1, first strand: chain 'C' and resid 356 through 358 removed outlier: 3.501A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE3, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE4, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.187A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.622A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.701A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.701A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 734 through 735 Processing sheet with id=AE8, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE9, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AF1, first strand: chain 'D' and resid 10 through 13 removed outlier: 4.115A pdb=" N ALA D 13 " --> pdb=" O GLU D 105 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AF3, first strand: chain 'E' and resid 10 through 12 removed outlier: 8.600A pdb=" N TYR E 32 " --> pdb=" O ILE E 52 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ILE E 52 " --> pdb=" O TYR E 32 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE E 34 " --> pdb=" O ARG E 50 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ARG E 50 " --> pdb=" O PHE E 34 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AF5, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AF6, first strand: chain 'F' and resid 10 through 12 removed outlier: 6.651A pdb=" N LEU F 11 " --> pdb=" O GLU F 105 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AF8, first strand: chain 'G' and resid 10 through 12 removed outlier: 8.695A pdb=" N TYR G 32 " --> pdb=" O ILE G 52 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N ILE G 52 " --> pdb=" O TYR G 32 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N PHE G 34 " --> pdb=" O ARG G 50 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG G 50 " --> pdb=" O PHE G 34 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TRP G 36 " --> pdb=" O MET G 48 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.503A pdb=" N ASP G 110 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AG2, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.730A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AG4, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.365A pdb=" N GLU I 10 " --> pdb=" O THR I 118 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N TYR I 32 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N ILE I 52 " --> pdb=" O TYR I 32 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ARG I 50 " --> pdb=" O PHE I 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP I 36 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.365A pdb=" N GLU I 10 " --> pdb=" O THR I 118 " (cutoff:3.500A) 1245 hydrogen bonds defined for protein. 3285 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: 16.55 Time building geometry restraints manager: 14.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9580 1.34 - 1.46: 7726 1.46 - 1.59: 13453 1.59 - 1.71: 0 1.71 - 1.83: 168 Bond restraints: 30927 Sorted by residual: bond pdb=" N THR C 19 " pdb=" CA THR C 19 " ideal model delta sigma weight residual 1.459 1.488 -0.029 9.10e-03 1.21e+04 1.01e+01 bond pdb=" N VAL B 736 " pdb=" CA VAL B 736 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.18e-02 7.18e+03 9.52e+00 bond pdb=" N THR A 20 " pdb=" CA THR A 20 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.18e-02 7.18e+03 7.79e+00 bond pdb=" N LEU C 18 " pdb=" CA LEU C 18 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.21e-02 6.83e+03 7.13e+00 bond pdb=" N VAL C 16 " pdb=" CA VAL C 16 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.29e-02 6.01e+03 7.00e+00 ... (remaining 30922 not shown) Histogram of bond angle deviations from ideal: 98.11 - 105.30: 634 105.30 - 112.50: 15900 112.50 - 119.70: 9834 119.70 - 126.89: 15343 126.89 - 134.09: 327 Bond angle restraints: 42038 Sorted by residual: angle pdb=" CA GLY A 89 " pdb=" C GLY A 89 " pdb=" N VAL A 90 " ideal model delta sigma weight residual 114.86 118.38 -3.52 1.01e+00 9.80e-01 1.21e+01 angle pdb=" N MET B 740 " pdb=" CA MET B 740 " pdb=" C MET B 740 " ideal model delta sigma weight residual 113.23 109.07 4.16 1.24e+00 6.50e-01 1.12e+01 angle pdb=" N LYS A 528 " pdb=" CA LYS A 528 " pdb=" C LYS A 528 " ideal model delta sigma weight residual 113.89 108.64 5.25 1.58e+00 4.01e-01 1.10e+01 angle pdb=" N THR C 20 " pdb=" CA THR C 20 " pdb=" C THR C 20 " ideal model delta sigma weight residual 112.87 109.00 3.87 1.20e+00 6.94e-01 1.04e+01 angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 114.53 -3.83 1.22e+00 6.72e-01 9.85e+00 ... (remaining 42033 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 17325 17.56 - 35.11: 1319 35.11 - 52.67: 276 52.67 - 70.23: 55 70.23 - 87.78: 37 Dihedral angle restraints: 19012 sinusoidal: 7993 harmonic: 11019 Sorted by residual: 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 -6.19 -79.81 1 1.00e+01 1.00e-02 7.90e+01 dihedral pdb=" CB CYS D 23 " pdb=" SG CYS D 23 " pdb=" SG CYS D 88 " pdb=" CB CYS D 88 " ideal model delta sinusoidal sigma weight residual 93.00 162.58 -69.58 1 1.00e+01 1.00e-02 6.25e+01 dihedral pdb=" CB CYS F 23 " pdb=" SG CYS F 23 " pdb=" SG CYS F 88 " pdb=" CB CYS F 88 " ideal model delta sinusoidal sigma weight residual 93.00 156.62 -63.62 1 1.00e+01 1.00e-02 5.33e+01 ... (remaining 19009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 4412 0.087 - 0.174: 440 0.174 - 0.260: 8 0.260 - 0.347: 0 0.347 - 0.434: 1 Chirality restraints: 4861 Sorted by residual: chirality pdb=" C1 NAG A1305 " pdb=" ND2 ASN A 709 " pdb=" C2 NAG A1305 " pdb=" O5 NAG A1305 " both_signs ideal model delta sigma weight residual False -2.40 -1.97 -0.43 2.00e-01 2.50e+01 4.71e+00 chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C1 NAG B1303 " pdb=" ND2 ASN B 282 " pdb=" C2 NAG B1303 " pdb=" O5 NAG B1303 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 4858 not shown) Planarity restraints: 5383 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.038 5.00e-02 4.00e+02 5.72e-02 5.24e+00 pdb=" N PRO C 987 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER F 7 " 0.036 5.00e-02 4.00e+02 5.45e-02 4.74e+00 pdb=" N PRO F 8 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO F 8 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO F 8 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 52 " 0.035 5.00e-02 4.00e+02 5.31e-02 4.51e+00 pdb=" N PRO G 53 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " 0.030 5.00e-02 4.00e+02 ... (remaining 5380 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 494 2.67 - 3.22: 27802 3.22 - 3.78: 44920 3.78 - 4.34: 60548 4.34 - 4.90: 101865 Nonbonded interactions: 235629 Sorted by model distance: nonbonded pdb=" OG SER F 26 " pdb=" OE1 GLN F 27 " model vdw 2.107 3.040 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.226 3.040 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.234 3.040 nonbonded pdb=" OE2 GLU B 156 " pdb=" NH1 ARG B 158 " model vdw 2.249 3.120 nonbonded pdb=" OH TYR H 94 " pdb=" OD1 ASN I 59 " model vdw 2.251 3.040 ... (remaining 235624 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 15 through 827 or resid 853 through 1147 or resid 1301 thr \ ough 1305)) selection = (chain 'C' and (resid 15 through 827 or resid 853 through 1147 or resid 1301 thr \ ough 1305)) } ncs_group { reference = (chain 'D' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 108)) selection = chain 'F' selection = (chain 'H' and (resid 1 through 17 or (resid 18 and (name N or name CA or name C \ or name O or name CB )) or resid 19 through 108)) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } 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: 54.540 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 81.720 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 30927 Z= 0.209 Angle : 0.603 8.818 42038 Z= 0.331 Chirality : 0.046 0.434 4861 Planarity : 0.004 0.057 5354 Dihedral : 13.202 87.783 11784 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.14 (0.14), residues: 3725 helix: 2.20 (0.21), residues: 660 sheet: 0.65 (0.16), residues: 1032 loop : -0.96 (0.13), residues: 2033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 111 HIS 0.003 0.000 HIS C 954 PHE 0.021 0.001 PHE A 515 TYR 0.025 0.001 TYR C 904 ARG 0.007 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 3.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 PHE cc_start: 0.8721 (m-80) cc_final: 0.8390 (m-80) REVERT: B 740 MET cc_start: 0.8636 (tmm) cc_final: 0.8358 (tmm) REVERT: D 45 LYS cc_start: 0.7807 (mmtm) cc_final: 0.7560 (mmtm) REVERT: E 110 ASP cc_start: 0.7369 (t70) cc_final: 0.7145 (t0) REVERT: F 55 GLU cc_start: 0.8508 (tp30) cc_final: 0.8058 (tp30) REVERT: F 103 LYS cc_start: 0.9151 (tptt) cc_final: 0.8884 (tptp) REVERT: G 101 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8297 (tm-30) REVERT: I 74 LYS cc_start: 0.8416 (tppt) cc_final: 0.8020 (tptt) outliers start: 0 outliers final: 0 residues processed: 289 average time/residue: 0.4261 time to fit residues: 197.1747 Evaluate side-chains 200 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 3.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 316 optimal weight: 7.9990 chunk 284 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 293 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 178 optimal weight: 0.0870 chunk 218 optimal weight: 3.9990 chunk 340 optimal weight: 0.0000 overall best weight: 1.6168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 115 GLN A 188 ASN A 487 ASN A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 935 GLN C1010 GLN D 37 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.0977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 30927 Z= 0.222 Angle : 0.556 10.324 42038 Z= 0.288 Chirality : 0.045 0.417 4861 Planarity : 0.004 0.070 5354 Dihedral : 6.264 58.103 4975 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.61 % Allowed : 6.63 % Favored : 92.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.13 (0.14), residues: 3725 helix: 2.12 (0.21), residues: 667 sheet: 0.60 (0.16), residues: 1031 loop : -0.91 (0.13), residues: 2027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 36 HIS 0.004 0.001 HIS B1058 PHE 0.022 0.001 PHE C 559 TYR 0.022 0.001 TYR F 49 ARG 0.005 0.000 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 215 time to evaluate : 3.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.8733 (tmm) cc_final: 0.8407 (tmm) REVERT: C 269 TYR cc_start: 0.7592 (m-80) cc_final: 0.7336 (m-80) REVERT: F 103 LYS cc_start: 0.9168 (tptt) cc_final: 0.8916 (tptp) REVERT: G 101 GLU cc_start: 0.8640 (tm-30) cc_final: 0.8429 (tm-30) REVERT: H 70 GLU cc_start: 0.8170 (tp30) cc_final: 0.7877 (tp30) REVERT: H 82 ASP cc_start: 0.7851 (m-30) cc_final: 0.7462 (m-30) REVERT: H 104 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7906 (mt) REVERT: I 74 LYS cc_start: 0.8404 (tppt) cc_final: 0.8020 (tptt) REVERT: I 98 ARG cc_start: 0.8112 (ttp80) cc_final: 0.7188 (ttp80) outliers start: 20 outliers final: 12 residues processed: 228 average time/residue: 0.4280 time to fit residues: 160.4027 Evaluate side-chains 201 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 188 time to evaluate : 3.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain I residue 57 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 189 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 231 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 341 optimal weight: 3.9990 chunk 368 optimal weight: 0.8980 chunk 303 optimal weight: 2.9990 chunk 338 optimal weight: 30.0000 chunk 116 optimal weight: 8.9990 chunk 273 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN B 762 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 30927 Z= 0.290 Angle : 0.560 8.599 42038 Z= 0.293 Chirality : 0.045 0.446 4861 Planarity : 0.004 0.067 5354 Dihedral : 5.855 56.769 4975 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.88 % Allowed : 9.59 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.03 (0.14), residues: 3725 helix: 2.08 (0.21), residues: 665 sheet: 0.58 (0.16), residues: 1002 loop : -1.00 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 36 HIS 0.005 0.001 HIS B1058 PHE 0.028 0.001 PHE C 559 TYR 0.025 0.001 TYR G 32 ARG 0.005 0.000 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 211 time to evaluate : 3.738 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 456 PHE cc_start: 0.8625 (m-80) cc_final: 0.8217 (m-80) REVERT: B 740 MET cc_start: 0.8714 (tmm) cc_final: 0.8270 (tmm) REVERT: C 170 TYR cc_start: 0.8426 (t80) cc_final: 0.8087 (t80) REVERT: G 101 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8431 (tm-30) REVERT: H 70 GLU cc_start: 0.8286 (tp30) cc_final: 0.8024 (tp30) REVERT: I 74 LYS cc_start: 0.8361 (tppt) cc_final: 0.7962 (tptt) REVERT: I 98 ARG cc_start: 0.8145 (ttp80) cc_final: 0.7187 (ttp80) outliers start: 29 outliers final: 16 residues processed: 229 average time/residue: 0.4393 time to fit residues: 163.5444 Evaluate side-chains 201 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 185 time to evaluate : 3.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 71 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 337 optimal weight: 20.0000 chunk 256 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 162 optimal weight: 0.9990 chunk 229 optimal weight: 5.9990 chunk 342 optimal weight: 0.4980 chunk 362 optimal weight: 2.9990 chunk 178 optimal weight: 0.0470 chunk 324 optimal weight: 30.0000 chunk 97 optimal weight: 3.9990 overall best weight: 1.7084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 450 ASN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 30927 Z= 0.222 Angle : 0.534 6.742 42038 Z= 0.278 Chirality : 0.045 0.439 4861 Planarity : 0.004 0.064 5354 Dihedral : 5.448 56.398 4975 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.15 % Allowed : 10.35 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.08 (0.14), residues: 3725 helix: 2.10 (0.21), residues: 674 sheet: 0.65 (0.16), residues: 996 loop : -1.00 (0.13), residues: 2055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 36 HIS 0.003 0.001 HIS B1058 PHE 0.024 0.001 PHE C 559 TYR 0.021 0.001 TYR F 49 ARG 0.004 0.000 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 204 time to evaluate : 3.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.8639 (m-80) cc_final: 0.8240 (m-80) REVERT: C 170 TYR cc_start: 0.8434 (t80) cc_final: 0.8141 (t80) REVERT: C 269 TYR cc_start: 0.7503 (m-80) cc_final: 0.7196 (m-80) REVERT: F 103 LYS cc_start: 0.9223 (tptt) cc_final: 0.8924 (tppt) REVERT: G 62 GLN cc_start: 0.8688 (tp40) cc_final: 0.8244 (tp40) REVERT: G 65 GLN cc_start: 0.8224 (pm20) cc_final: 0.7999 (mp10) REVERT: G 101 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8376 (tm-30) REVERT: H 70 GLU cc_start: 0.8280 (tp30) cc_final: 0.7970 (tp30) REVERT: H 104 LEU cc_start: 0.8357 (tp) cc_final: 0.8157 (mt) REVERT: I 74 LYS cc_start: 0.8304 (tppt) cc_final: 0.7905 (tptt) REVERT: I 98 ARG cc_start: 0.8123 (ttp80) cc_final: 0.7169 (ttp80) outliers start: 38 outliers final: 27 residues processed: 230 average time/residue: 0.4169 time to fit residues: 159.0003 Evaluate side-chains 215 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 188 time to evaluate : 3.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 105 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 269 optimal weight: 1.9990 chunk 149 optimal weight: 0.9980 chunk 309 optimal weight: 7.9990 chunk 250 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 185 optimal weight: 6.9990 chunk 325 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 ASN A 613 GLN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 30927 Z= 0.316 Angle : 0.572 8.717 42038 Z= 0.297 Chirality : 0.045 0.464 4861 Planarity : 0.004 0.063 5354 Dihedral : 5.349 55.957 4975 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.75 % Allowed : 11.32 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.01 (0.14), residues: 3725 helix: 2.03 (0.21), residues: 668 sheet: 0.67 (0.16), residues: 966 loop : -1.06 (0.13), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 36 HIS 0.005 0.001 HIS C1058 PHE 0.029 0.002 PHE C 559 TYR 0.021 0.001 TYR F 49 ARG 0.004 0.000 ARG C 815 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 199 time to evaluate : 3.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.8669 (m-80) cc_final: 0.8280 (m-80) REVERT: C 170 TYR cc_start: 0.8538 (t80) cc_final: 0.8305 (t80) REVERT: F 103 LYS cc_start: 0.9242 (tptt) cc_final: 0.8936 (tppt) REVERT: G 101 GLU cc_start: 0.8743 (tm-30) cc_final: 0.8399 (tm-30) REVERT: H 70 GLU cc_start: 0.8276 (tp30) cc_final: 0.7904 (tp30) REVERT: I 50 ARG cc_start: 0.9256 (ttp-110) cc_final: 0.9005 (ttp80) REVERT: I 74 LYS cc_start: 0.8261 (tppt) cc_final: 0.7847 (tptt) REVERT: I 98 ARG cc_start: 0.8169 (ttp80) cc_final: 0.7134 (ttp80) outliers start: 58 outliers final: 45 residues processed: 242 average time/residue: 0.4322 time to fit residues: 172.4104 Evaluate side-chains 228 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 183 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 96 CYS Chi-restraints excluded: chain I residue 105 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 6.9990 chunk 326 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 212 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 362 optimal weight: 5.9990 chunk 301 optimal weight: 1.9990 chunk 167 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 190 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 30927 Z= 0.177 Angle : 0.526 7.541 42038 Z= 0.272 Chirality : 0.044 0.431 4861 Planarity : 0.004 0.062 5354 Dihedral : 5.028 55.932 4975 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.45 % Allowed : 11.98 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.10 (0.14), residues: 3725 helix: 2.22 (0.21), residues: 666 sheet: 0.72 (0.16), residues: 990 loop : -1.04 (0.13), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 36 HIS 0.002 0.001 HIS C 505 PHE 0.020 0.001 PHE C 559 TYR 0.021 0.001 TYR F 49 ARG 0.005 0.000 ARG E 87 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 212 time to evaluate : 3.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8268 (t80) cc_final: 0.8055 (t80) REVERT: A 423 TYR cc_start: 0.5809 (t80) cc_final: 0.5597 (t80) REVERT: A 448 ASN cc_start: 0.8588 (t0) cc_final: 0.7742 (p0) REVERT: B 456 PHE cc_start: 0.8679 (m-80) cc_final: 0.8312 (m-80) REVERT: C 170 TYR cc_start: 0.8526 (t80) cc_final: 0.8307 (t80) REVERT: F 103 LYS cc_start: 0.9243 (tptt) cc_final: 0.8936 (tppt) REVERT: G 101 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8378 (tm-30) REVERT: H 70 GLU cc_start: 0.8239 (tp30) cc_final: 0.7817 (tp30) REVERT: I 46 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7720 (pt0) REVERT: I 50 ARG cc_start: 0.9210 (ttp-110) cc_final: 0.8934 (ttp80) REVERT: I 87 ARG cc_start: 0.9212 (ttm-80) cc_final: 0.8929 (ttm-80) REVERT: I 98 ARG cc_start: 0.8126 (ttp80) cc_final: 0.7741 (ttp80) outliers start: 48 outliers final: 35 residues processed: 247 average time/residue: 0.4266 time to fit residues: 170.8115 Evaluate side-chains 231 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 196 time to evaluate : 3.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 57 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 206 optimal weight: 30.0000 chunk 264 optimal weight: 6.9990 chunk 205 optimal weight: 0.9980 chunk 305 optimal weight: 1.9990 chunk 202 optimal weight: 0.8980 chunk 361 optimal weight: 3.9990 chunk 226 optimal weight: 30.0000 chunk 220 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 30927 Z= 0.272 Angle : 0.559 8.462 42038 Z= 0.291 Chirality : 0.045 0.448 4861 Planarity : 0.004 0.062 5354 Dihedral : 5.035 55.833 4975 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.69 % Allowed : 12.50 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.05 (0.14), residues: 3725 helix: 2.20 (0.21), residues: 661 sheet: 0.66 (0.16), residues: 987 loop : -1.05 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 36 HIS 0.004 0.001 HIS C1058 PHE 0.025 0.001 PHE C 559 TYR 0.020 0.001 TYR F 49 ARG 0.005 0.000 ARG C 765 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 197 time to evaluate : 3.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8301 (t80) cc_final: 0.8080 (t80) REVERT: A 448 ASN cc_start: 0.8631 (t0) cc_final: 0.7818 (p0) REVERT: B 456 PHE cc_start: 0.8691 (m-80) cc_final: 0.8313 (m-80) REVERT: C 170 TYR cc_start: 0.8553 (t80) cc_final: 0.8349 (t80) REVERT: F 45 LYS cc_start: 0.9062 (tppt) cc_final: 0.8856 (tppt) REVERT: F 103 LYS cc_start: 0.9243 (tptt) cc_final: 0.8961 (tppt) REVERT: G 101 GLU cc_start: 0.8760 (tm-30) cc_final: 0.8409 (tm-30) REVERT: H 70 GLU cc_start: 0.8289 (tp30) cc_final: 0.7835 (tp30) REVERT: I 46 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7629 (pt0) REVERT: I 87 ARG cc_start: 0.9189 (ttm-80) cc_final: 0.8946 (ttm-80) REVERT: I 98 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7264 (ttp80) outliers start: 56 outliers final: 44 residues processed: 240 average time/residue: 0.4323 time to fit residues: 169.3763 Evaluate side-chains 234 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 190 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 959 LEU Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 57 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 6.9990 chunk 144 optimal weight: 10.0000 chunk 215 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 70 optimal weight: 0.0170 chunk 229 optimal weight: 2.9990 chunk 246 optimal weight: 4.9990 chunk 178 optimal weight: 4.9990 chunk 33 optimal weight: 9.9990 chunk 284 optimal weight: 1.9990 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 30927 Z= 0.196 Angle : 0.541 8.686 42038 Z= 0.280 Chirality : 0.044 0.431 4861 Planarity : 0.004 0.061 5354 Dihedral : 4.896 55.796 4975 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.57 % Allowed : 12.98 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: 0.10 (0.14), residues: 3725 helix: 2.24 (0.21), residues: 666 sheet: 0.71 (0.16), residues: 991 loop : -1.04 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 36 HIS 0.002 0.001 HIS B1058 PHE 0.021 0.001 PHE C 559 TYR 0.020 0.001 TYR F 49 ARG 0.007 0.000 ARG I 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 207 time to evaluate : 3.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 TYR cc_start: 0.8272 (t80) cc_final: 0.8048 (t80) REVERT: A 448 ASN cc_start: 0.8620 (t0) cc_final: 0.7849 (p0) REVERT: B 456 PHE cc_start: 0.8699 (m-80) cc_final: 0.8338 (m-80) REVERT: C 170 TYR cc_start: 0.8569 (t80) cc_final: 0.8358 (t80) REVERT: D 62 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7897 (m-10) REVERT: E 110 ASP cc_start: 0.7648 (t70) cc_final: 0.7418 (t0) REVERT: F 42 LYS cc_start: 0.9431 (mtpp) cc_final: 0.9072 (ptpp) REVERT: F 45 LYS cc_start: 0.9054 (tppt) cc_final: 0.8852 (tppt) REVERT: F 103 LYS cc_start: 0.9248 (tptt) cc_final: 0.8926 (tppt) REVERT: G 101 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8413 (tm-30) REVERT: H 70 GLU cc_start: 0.8155 (tp30) cc_final: 0.7597 (tp30) REVERT: I 46 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7654 (pt0) REVERT: I 82 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8463 (tp30) REVERT: I 87 ARG cc_start: 0.9183 (ttm-80) cc_final: 0.8945 (ttm-80) REVERT: I 98 ARG cc_start: 0.8134 (ttp80) cc_final: 0.7225 (ttp80) outliers start: 52 outliers final: 42 residues processed: 244 average time/residue: 0.4566 time to fit residues: 182.7914 Evaluate side-chains 240 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 197 time to evaluate : 3.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 753 LEU Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 62 PHE Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 57 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 50.0000 chunk 346 optimal weight: 7.9990 chunk 315 optimal weight: 8.9990 chunk 336 optimal weight: 9.9990 chunk 202 optimal weight: 0.8980 chunk 146 optimal weight: 4.9990 chunk 264 optimal weight: 4.9990 chunk 103 optimal weight: 30.0000 chunk 304 optimal weight: 1.9990 chunk 318 optimal weight: 7.9990 chunk 335 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 901 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.074 30927 Z= 0.489 Angle : 0.681 7.562 42038 Z= 0.354 Chirality : 0.048 0.509 4861 Planarity : 0.004 0.061 5354 Dihedral : 5.424 57.395 4975 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.75 % Allowed : 13.37 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.26 (0.13), residues: 3725 helix: 1.86 (0.21), residues: 658 sheet: 0.44 (0.16), residues: 992 loop : -1.20 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 36 HIS 0.006 0.001 HIS C1058 PHE 0.036 0.002 PHE C 559 TYR 0.024 0.002 TYR A 904 ARG 0.006 0.001 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 188 time to evaluate : 3.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 ASN cc_start: 0.8714 (t0) cc_final: 0.7848 (p0) REVERT: B 456 PHE cc_start: 0.8719 (m-80) cc_final: 0.8329 (m-80) REVERT: C 1002 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7857 (tm-30) REVERT: E 110 ASP cc_start: 0.7683 (t70) cc_final: 0.7420 (t0) REVERT: F 42 LYS cc_start: 0.9461 (mtpp) cc_final: 0.9250 (mtmm) REVERT: F 45 LYS cc_start: 0.9032 (tppt) cc_final: 0.8816 (tppt) REVERT: G 101 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8425 (tm-30) REVERT: I 98 ARG cc_start: 0.8149 (ttp80) cc_final: 0.7193 (ttp80) outliers start: 58 outliers final: 47 residues processed: 231 average time/residue: 0.4119 time to fit residues: 156.7761 Evaluate side-chains 226 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 178 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 977 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 1002 GLN Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain I residue 57 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 1.9990 chunk 356 optimal weight: 5.9990 chunk 217 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 247 optimal weight: 6.9990 chunk 373 optimal weight: 3.9990 chunk 343 optimal weight: 7.9990 chunk 297 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 229 optimal weight: 0.9990 chunk 182 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 30927 Z= 0.234 Angle : 0.578 8.160 42038 Z= 0.301 Chirality : 0.046 0.457 4861 Planarity : 0.004 0.061 5354 Dihedral : 5.184 55.849 4975 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 1.39 % Allowed : 13.92 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.13 (0.14), residues: 3725 helix: 2.04 (0.21), residues: 658 sheet: 0.49 (0.16), residues: 999 loop : -1.14 (0.13), residues: 2068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 258 HIS 0.003 0.001 HIS A1058 PHE 0.024 0.001 PHE C 559 TYR 0.021 0.001 TYR A 904 ARG 0.006 0.000 ARG I 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7450 Ramachandran restraints generated. 3725 Oldfield, 0 Emsley, 3725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 199 time to evaluate : 3.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 ASN cc_start: 0.8695 (t0) cc_final: 0.7858 (p0) REVERT: B 456 PHE cc_start: 0.8684 (m-80) cc_final: 0.8299 (m-80) REVERT: E 110 ASP cc_start: 0.7664 (t70) cc_final: 0.7433 (t0) REVERT: G 38 ARG cc_start: 0.7329 (tpp80) cc_final: 0.6947 (tpt170) REVERT: G 101 GLU cc_start: 0.8805 (tm-30) cc_final: 0.8412 (tm-30) REVERT: I 98 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7163 (ttp80) outliers start: 46 outliers final: 41 residues processed: 234 average time/residue: 0.4262 time to fit residues: 163.8612 Evaluate side-chains 230 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 189 time to evaluate : 3.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 994 ASP Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 762 GLN Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 362 VAL Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 48 MET Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 82 GLU Chi-restraints excluded: chain H residue 10 THR Chi-restraints excluded: chain I residue 57 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 3.9990 chunk 316 optimal weight: 30.0000 chunk 91 optimal weight: 3.9990 chunk 274 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 297 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 305 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** D 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.077262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.049693 restraints weight = 107017.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.051604 restraints weight = 53098.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.052832 restraints weight = 34917.938| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 30927 Z= 0.359 Angle : 0.621 7.663 42038 Z= 0.322 Chirality : 0.046 0.471 4861 Planarity : 0.004 0.060 5354 Dihedral : 5.263 55.843 4975 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.45 % Allowed : 13.98 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.54 % 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: -0.21 (0.14), residues: 3725 helix: 1.98 (0.21), residues: 658 sheet: 0.44 (0.16), residues: 992 loop : -1.19 (0.13), residues: 2075 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 258 HIS 0.005 0.001 HIS C1058 PHE 0.029 0.002 PHE C 559 TYR 0.022 0.001 TYR A 904 ARG 0.016 0.001 ARG E 67 Origin is already at (0, 0, 0), no shifts will be applied Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: