Starting phenix.real_space_refine on Wed Feb 21 09:38:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwi_32866/02_2024/7wwi_32866.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwi_32866/02_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_32866/02_2024/7wwi_32866.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwi_32866/02_2024/7wwi_32866.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwi_32866/02_2024/7wwi_32866.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wwi_32866/02_2024/7wwi_32866.pdb" } 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-5238/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: 16.18, per 1000 atoms: 0.54 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: 11.46 Conformation dependent library (CDL) restraints added in 5.6 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: 4.18 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: 13.73 Time building geometry restraints manager: 12.36 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 2.440 nonbonded pdb=" OG1 THR C 109 " pdb=" OD1 ASP C 111 " model vdw 2.226 2.440 nonbonded pdb=" OG1 THR A 323 " pdb=" OE1 GLU A 324 " model vdw 2.234 2.440 nonbonded pdb=" OE2 GLU B 156 " pdb=" NH1 ARG B 158 " model vdw 2.249 2.520 nonbonded pdb=" OH TYR H 94 " pdb=" OD1 ASN I 59 " model vdw 2.251 2.440 ... (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 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: 11.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 37.940 Check model and map are aligned: 0.530 Set scattering table: 0.280 Process input model: 80.600 Find NCS groups from input model: 2.200 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.940 ------------------------------------------------------------------------------- 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 : 3.352 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: 0.4262 time to fit residues: 196.1015 Evaluate side-chains 200 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 200 time to evaluate : 3.290 ------------------------------------------------------------------------------- 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: 8.9990 chunk 284 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 191 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 293 optimal weight: 2.9990 chunk 113 optimal weight: 8.9990 chunk 178 optimal weight: 8.9990 chunk 218 optimal weight: 6.9990 chunk 340 optimal weight: 0.0970 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 762 GLN A 957 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN C 804 GLN C 935 GLN ** C 978 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1010 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 30927 Z= 0.295 Angle : 0.565 9.953 42038 Z= 0.293 Chirality : 0.045 0.425 4861 Planarity : 0.004 0.072 5354 Dihedral : 6.439 58.022 4975 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.79 % Allowed : 7.02 % Favored : 92.19 % 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: 0.09 (0.14), residues: 3725 helix: 2.18 (0.21), residues: 657 sheet: 0.59 (0.16), residues: 1026 loop : -0.97 (0.13), residues: 2042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 36 HIS 0.004 0.001 HIS B1058 PHE 0.024 0.001 PHE C 559 TYR 0.021 0.001 TYR F 49 ARG 0.007 0.000 ARG B1107 *********************** 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 234 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 208 time to evaluate : 3.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.8809 (tmm) cc_final: 0.8575 (tmm) REVERT: F 103 LYS cc_start: 0.9157 (tptt) cc_final: 0.8897 (tptp) REVERT: G 101 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8452 (tm-30) REVERT: H 70 GLU cc_start: 0.8167 (tp30) cc_final: 0.7900 (tp30) REVERT: I 74 LYS cc_start: 0.8413 (tppt) cc_final: 0.8044 (tptt) outliers start: 26 outliers final: 18 residues processed: 222 average time/residue: 0.4019 time to fit residues: 147.2891 Evaluate side-chains 208 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 190 time to evaluate : 3.204 ------------------------------------------------------------------------------- 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 392 PHE Chi-restraints excluded: chain B residue 481 ASN 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 55 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain H residue 104 LEU Chi-restraints excluded: chain I residue 35 ILE 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: 0.9980 chunk 105 optimal weight: 0.9980 chunk 283 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 93 optimal weight: 0.9980 chunk 341 optimal weight: 20.0000 chunk 368 optimal weight: 0.9980 chunk 303 optimal weight: 2.9990 chunk 338 optimal weight: 20.0000 chunk 116 optimal weight: 10.0000 chunk 273 optimal weight: 4.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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 762 GLN ** B 334 ASN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 30927 Z= 0.191 Angle : 0.516 8.019 42038 Z= 0.268 Chirality : 0.044 0.418 4861 Planarity : 0.004 0.066 5354 Dihedral : 5.806 57.104 4975 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.85 % Allowed : 9.05 % Favored : 90.11 % 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: 2.23 (0.21), residues: 664 sheet: 0.62 (0.16), residues: 1014 loop : -0.96 (0.13), residues: 2047 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 36 HIS 0.003 0.001 HIS B1058 PHE 0.022 0.001 PHE C 559 TYR 0.021 0.001 TYR F 49 ARG 0.004 0.000 ARG A1107 *********************** 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 245 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 217 time to evaluate : 3.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.8754 (tmm) cc_final: 0.8434 (tmm) REVERT: C 170 TYR cc_start: 0.8361 (t80) cc_final: 0.8009 (t80) REVERT: F 42 LYS cc_start: 0.9435 (mtpp) cc_final: 0.9072 (ptpp) REVERT: F 103 LYS cc_start: 0.9179 (tptt) cc_final: 0.8907 (tppt) REVERT: G 62 GLN cc_start: 0.8685 (tp40) cc_final: 0.8312 (tp40) REVERT: G 101 GLU cc_start: 0.8653 (tm-30) cc_final: 0.8428 (tm-30) REVERT: H 70 GLU cc_start: 0.8165 (tp30) cc_final: 0.7931 (tp30) REVERT: I 74 LYS cc_start: 0.8351 (tppt) cc_final: 0.8000 (tptt) outliers start: 28 outliers final: 16 residues processed: 233 average time/residue: 0.4589 time to fit residues: 172.9127 Evaluate side-chains 208 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 192 time to evaluate : 3.779 ------------------------------------------------------------------------------- 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 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 745 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain G residue 71 THR 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: 0.6980 chunk 177 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 162 optimal weight: 4.9990 chunk 229 optimal weight: 4.9990 chunk 342 optimal weight: 20.0000 chunk 362 optimal weight: 7.9990 chunk 178 optimal weight: 0.5980 chunk 324 optimal weight: 0.0470 chunk 97 optimal weight: 4.9990 overall best weight: 2.2682 ------------------------------------------------------------------------------- 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 ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 474 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 30927 Z= 0.280 Angle : 0.545 7.925 42038 Z= 0.283 Chirality : 0.045 0.440 4861 Planarity : 0.004 0.065 5354 Dihedral : 5.567 56.432 4975 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 0.97 % Allowed : 10.77 % Favored : 88.26 % 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: 0.11 (0.14), residues: 3725 helix: 2.19 (0.21), residues: 664 sheet: 0.66 (0.16), residues: 975 loop : -0.96 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 36 HIS 0.004 0.001 HIS B1058 PHE 0.026 0.001 PHE C 559 TYR 0.022 0.001 TYR F 49 ARG 0.007 0.000 ARG B1107 *********************** 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 233 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 201 time to evaluate : 3.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.8606 (m-80) cc_final: 0.8119 (m-80) REVERT: B 740 MET cc_start: 0.8772 (tmm) cc_final: 0.8376 (tmm) REVERT: C 170 TYR cc_start: 0.8430 (t80) cc_final: 0.8107 (t80) REVERT: F 103 LYS cc_start: 0.9221 (tptt) cc_final: 0.8936 (tppt) REVERT: G 101 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8445 (tm-30) REVERT: H 70 GLU cc_start: 0.8210 (tp30) cc_final: 0.7913 (tp30) REVERT: I 74 LYS cc_start: 0.8361 (tppt) cc_final: 0.8025 (tptt) outliers start: 32 outliers final: 26 residues processed: 222 average time/residue: 0.4252 time to fit residues: 152.9617 Evaluate side-chains 212 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 186 time to evaluate : 3.572 ------------------------------------------------------------------------------- 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 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 408 ARG Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 1141 LEU Chi-restraints excluded: chain C residue 242 LEU 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 F residue 82 ASP Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain I residue 57 ILE Chi-restraints excluded: chain I residue 71 THR Chi-restraints excluded: chain I residue 76 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 301 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 269 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 309 optimal weight: 7.9990 chunk 250 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 185 optimal weight: 0.8980 chunk 325 optimal weight: 8.9990 chunk 91 optimal weight: 0.9990 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** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 658 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 30927 Z= 0.287 Angle : 0.551 6.671 42038 Z= 0.287 Chirality : 0.045 0.449 4861 Planarity : 0.004 0.064 5354 Dihedral : 5.384 56.207 4975 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.72 % Allowed : 11.50 % Favored : 86.78 % 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: 0.06 (0.14), residues: 3725 helix: 2.14 (0.21), residues: 659 sheet: 0.64 (0.17), residues: 980 loop : -1.00 (0.13), residues: 2086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 36 HIS 0.004 0.001 HIS C1058 PHE 0.026 0.001 PHE C 559 TYR 0.021 0.001 TYR F 49 ARG 0.004 0.000 ARG A1107 *********************** 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 264 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 207 time to evaluate : 3.776 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: 0.8633 (m-80) cc_final: 0.8158 (m-80) REVERT: B 740 MET cc_start: 0.8760 (tmm) cc_final: 0.8293 (tmm) REVERT: B 752 LEU cc_start: 0.9376 (mp) cc_final: 0.9143 (tt) REVERT: C 170 TYR cc_start: 0.8518 (t80) cc_final: 0.8263 (t80) REVERT: F 103 LYS cc_start: 0.9241 (tptt) cc_final: 0.8945 (tppt) REVERT: G 65 GLN cc_start: 0.8217 (mp10) cc_final: 0.8009 (mp10) REVERT: G 101 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8407 (tm-30) REVERT: H 70 GLU cc_start: 0.8168 (tp30) cc_final: 0.7781 (tp30) REVERT: I 74 LYS cc_start: 0.8310 (tppt) cc_final: 0.7957 (tptt) outliers start: 57 outliers final: 41 residues processed: 252 average time/residue: 0.4028 time to fit residues: 167.8553 Evaluate side-chains 234 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 193 time to evaluate : 3.300 ------------------------------------------------------------------------------- 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 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 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 29 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 599 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain G residue 71 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 76 THR Chi-restraints excluded: chain I residue 96 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 121 optimal weight: 4.9990 chunk 326 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 212 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 362 optimal weight: 8.9990 chunk 301 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 120 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 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: 0.8574 moved from start: 0.1717 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= 0.201 Angle : 0.526 9.049 42038 Z= 0.272 Chirality : 0.044 0.431 4861 Planarity : 0.004 0.062 5354 Dihedral : 5.139 55.873 4975 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.48 % Allowed : 12.34 % Favored : 86.17 % 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: 2.29 (0.21), residues: 658 sheet: 0.69 (0.16), residues: 990 loop : -0.98 (0.13), residues: 2077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 36 HIS 0.002 0.001 HIS C 505 PHE 0.022 0.001 PHE C 559 TYR 0.021 0.001 TYR F 49 ARG 0.003 0.000 ARG H 24 *********************** 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: 49 poor density : 211 time to evaluate : 3.604 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: 0.8627 (m-80) cc_final: 0.8171 (m-80) REVERT: B 740 MET cc_start: 0.8717 (tmm) cc_final: 0.8229 (tmm) REVERT: C 170 TYR cc_start: 0.8510 (t80) cc_final: 0.8271 (t80) REVERT: F 103 LYS cc_start: 0.9233 (tptt) cc_final: 0.8948 (tppt) REVERT: G 101 GLU cc_start: 0.8680 (tm-30) cc_final: 0.8375 (tm-30) REVERT: H 70 GLU cc_start: 0.8168 (tp30) cc_final: 0.7802 (tp30) REVERT: I 74 LYS cc_start: 0.8318 (tppt) cc_final: 0.7969 (tptt) outliers start: 49 outliers final: 41 residues processed: 248 average time/residue: 0.4274 time to fit residues: 173.4499 Evaluate side-chains 237 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 196 time to evaluate : 3.507 ------------------------------------------------------------------------------- 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 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 745 ASP Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 350 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 1077 THR Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain D residue 33 LEU 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 F residue 82 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 81 MET 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 76 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 349 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 206 optimal weight: 30.0000 chunk 264 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 305 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 361 optimal weight: 6.9990 chunk 226 optimal weight: 3.9990 chunk 220 optimal weight: 9.9990 chunk 166 optimal weight: 4.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN C 23 GLN ** 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 30927 Z= 0.256 Angle : 0.548 8.265 42038 Z= 0.283 Chirality : 0.044 0.440 4861 Planarity : 0.004 0.062 5354 Dihedral : 5.103 57.111 4975 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.88 % Allowed : 12.80 % Favored : 85.33 % 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: 0.09 (0.14), residues: 3725 helix: 2.26 (0.21), residues: 658 sheet: 0.69 (0.16), residues: 980 loop : -1.03 (0.13), residues: 2087 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 36 HIS 0.003 0.001 HIS C1058 PHE 0.023 0.001 PHE C 559 TYR 0.020 0.001 TYR F 49 ARG 0.003 0.000 ARG G 38 *********************** 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 267 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 205 time to evaluate : 3.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 423 TYR cc_start: 0.5943 (t80) cc_final: 0.5715 (t80) REVERT: A 448 ASN cc_start: 0.8560 (t0) cc_final: 0.7705 (p0) REVERT: B 456 PHE cc_start: 0.8640 (m-80) cc_final: 0.8180 (m-80) REVERT: B 740 MET cc_start: 0.8736 (tmm) cc_final: 0.8155 (tmm) REVERT: C 170 TYR cc_start: 0.8541 (t80) cc_final: 0.8335 (t80) REVERT: C 239 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.8370 (tp40) REVERT: F 103 LYS cc_start: 0.9236 (tptt) cc_final: 0.8978 (tppt) REVERT: G 101 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8402 (tm-30) REVERT: H 70 GLU cc_start: 0.8183 (tp30) cc_final: 0.7756 (tp30) REVERT: I 74 LYS cc_start: 0.8290 (tppt) cc_final: 0.7950 (tptt) outliers start: 62 outliers final: 52 residues processed: 253 average time/residue: 0.4013 time to fit residues: 167.2437 Evaluate side-chains 243 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 190 time to evaluate : 3.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR 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 392 PHE Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 697 MET Chi-restraints excluded: chain A residue 742 ILE 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 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 544 ASN Chi-restraints excluded: chain B residue 745 ASP Chi-restraints excluded: chain B residue 763 LEU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 239 GLN 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 738 CYS Chi-restraints excluded: chain C residue 763 LEU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 1077 THR 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 E residue 55 LEU Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain G residue 71 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 76 THR Chi-restraints excluded: chain I residue 100 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 223 optimal weight: 3.9990 chunk 144 optimal weight: 0.0970 chunk 215 optimal weight: 9.9990 chunk 108 optimal weight: 10.0000 chunk 71 optimal weight: 0.7980 chunk 70 optimal weight: 0.1980 chunk 229 optimal weight: 0.4980 chunk 246 optimal weight: 4.9990 chunk 178 optimal weight: 0.3980 chunk 33 optimal weight: 6.9990 chunk 284 optimal weight: 1.9990 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 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: 0.8537 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 30927 Z= 0.136 Angle : 0.516 9.016 42038 Z= 0.266 Chirality : 0.044 0.401 4861 Planarity : 0.004 0.061 5354 Dihedral : 4.811 55.644 4975 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.36 % Allowed : 13.49 % Favored : 85.14 % 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: 0.22 (0.14), residues: 3725 helix: 2.40 (0.21), residues: 657 sheet: 0.76 (0.16), residues: 1011 loop : -0.97 (0.13), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.002 0.000 HIS B 66 PHE 0.015 0.001 PHE C 559 TYR 0.020 0.001 TYR F 49 ARG 0.003 0.000 ARG D 61 *********************** 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 262 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 3.904 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: A 170 TYR cc_start: 0.8237 (t80) cc_final: 0.8031 (t80) REVERT: A 448 ASN cc_start: 0.8538 (t0) cc_final: 0.7755 (p0) REVERT: F 103 LYS cc_start: 0.9244 (tptt) cc_final: 0.8941 (tppt) REVERT: G 101 GLU cc_start: 0.8683 (tm-30) cc_final: 0.8401 (tm-30) REVERT: H 70 GLU cc_start: 0.8131 (tp30) cc_final: 0.7704 (tp30) REVERT: I 74 LYS cc_start: 0.8297 (tppt) cc_final: 0.7964 (tptt) outliers start: 45 outliers final: 33 residues processed: 252 average time/residue: 0.4553 time to fit residues: 189.7843 Evaluate side-chains 233 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 200 time to evaluate : 3.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 697 MET 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 B residue 62 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 392 PHE 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 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL 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 1104 VAL Chi-restraints excluded: chain C residue 1128 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 82 ASP 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 76 THR Chi-restraints excluded: chain I residue 100 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 328 optimal weight: 30.0000 chunk 346 optimal weight: 0.9980 chunk 315 optimal weight: 0.4980 chunk 336 optimal weight: 0.6980 chunk 202 optimal weight: 2.9990 chunk 146 optimal weight: 7.9990 chunk 264 optimal weight: 0.7980 chunk 103 optimal weight: 30.0000 chunk 304 optimal weight: 0.9990 chunk 318 optimal weight: 40.0000 chunk 335 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 314 GLN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 613 GLN ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 6 GLN ** G 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 30927 Z= 0.157 Angle : 0.522 10.700 42038 Z= 0.267 Chirality : 0.044 0.404 4861 Planarity : 0.004 0.060 5354 Dihedral : 4.680 55.610 4975 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.45 % Allowed : 13.83 % Favored : 84.72 % 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: 0.27 (0.14), residues: 3725 helix: 2.38 (0.21), residues: 658 sheet: 0.81 (0.16), residues: 1008 loop : -0.93 (0.13), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 36 HIS 0.002 0.000 HIS B 66 PHE 0.017 0.001 PHE C 559 TYR 0.021 0.001 TYR F 49 ARG 0.003 0.000 ARG I 87 *********************** 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 252 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 204 time to evaluate : 3.400 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: A 448 ASN cc_start: 0.8596 (t0) cc_final: 0.7816 (p0) REVERT: C 239 GLN cc_start: 0.8625 (OUTLIER) cc_final: 0.8407 (tp40) REVERT: E 110 ASP cc_start: 0.7655 (t70) cc_final: 0.7423 (t0) REVERT: F 103 LYS cc_start: 0.9234 (tptt) cc_final: 0.8923 (tppt) REVERT: G 101 GLU cc_start: 0.8695 (tm-30) cc_final: 0.8415 (tm-30) REVERT: H 70 GLU cc_start: 0.8145 (tp30) cc_final: 0.7653 (tp30) REVERT: I 74 LYS cc_start: 0.8296 (tppt) cc_final: 0.7974 (tptt) outliers start: 48 outliers final: 39 residues processed: 242 average time/residue: 0.4029 time to fit residues: 161.3084 Evaluate side-chains 237 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 197 time to evaluate : 3.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL 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 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 392 PHE 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 29 THR Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 239 GLN 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 1104 VAL Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 55 LEU Chi-restraints excluded: chain F residue 69 THR Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 110 ASP 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 76 THR Chi-restraints excluded: chain I residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 221 optimal weight: 7.9990 chunk 356 optimal weight: 8.9990 chunk 217 optimal weight: 10.0000 chunk 168 optimal weight: 7.9990 chunk 247 optimal weight: 8.9990 chunk 373 optimal weight: 0.5980 chunk 343 optimal weight: 9.9990 chunk 297 optimal weight: 4.9990 chunk 30 optimal weight: 9.9990 chunk 229 optimal weight: 0.4980 chunk 182 optimal weight: 1.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 188 ASN ** 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 81 ASN ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 603 ASN B 658 ASN B 901 GLN ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 30927 Z= 0.377 Angle : 0.615 8.873 42038 Z= 0.318 Chirality : 0.046 0.465 4861 Planarity : 0.004 0.061 5354 Dihedral : 5.061 56.114 4975 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.45 % Allowed : 14.19 % Favored : 84.36 % 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: 2.09 (0.21), residues: 658 sheet: 0.68 (0.16), residues: 983 loop : -1.06 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 36 HIS 0.006 0.001 HIS A1058 PHE 0.029 0.002 PHE C 559 TYR 0.021 0.002 TYR A1067 ARG 0.006 0.000 ARG G 38 ********************** 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 244 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 196 time to evaluate : 3.878 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: A 448 ASN cc_start: 0.8615 (t0) cc_final: 0.7791 (p0) REVERT: B 456 PHE cc_start: 0.8668 (m-80) cc_final: 0.8208 (m-80) REVERT: C 239 GLN cc_start: 0.8488 (OUTLIER) cc_final: 0.8249 (tp40) REVERT: E 110 ASP cc_start: 0.7663 (t70) cc_final: 0.7430 (t0) REVERT: G 101 GLU cc_start: 0.8765 (tm-30) cc_final: 0.8408 (tm-30) REVERT: I 12 LYS cc_start: 0.8752 (mtpp) cc_final: 0.8400 (mtpp) REVERT: I 74 LYS cc_start: 0.8271 (tppt) cc_final: 0.7950 (tptt) outliers start: 48 outliers final: 41 residues processed: 234 average time/residue: 0.4192 time to fit residues: 161.9573 Evaluate side-chains 228 residues out of total 3306 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 186 time to evaluate : 3.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 697 MET 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 392 PHE 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 29 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 239 GLN 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 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 F residue 69 THR Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 71 THR Chi-restraints excluded: chain G residue 110 ASP 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 76 THR Chi-restraints excluded: chain I residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 375 random chunks: chunk 236 optimal weight: 0.9980 chunk 316 optimal weight: 30.0000 chunk 91 optimal weight: 2.9990 chunk 274 optimal weight: 2.9990 chunk 43 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 297 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 305 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 957 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 658 ASN ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.078040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.050030 restraints weight = 106668.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.052100 restraints weight = 49289.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.053421 restraints weight = 31236.449| |-----------------------------------------------------------------------------| r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 30927 Z= 0.236 Angle : 0.560 9.688 42038 Z= 0.288 Chirality : 0.045 0.434 4861 Planarity : 0.004 0.061 5354 Dihedral : 4.943 55.852 4975 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.42 % Allowed : 14.31 % Favored : 84.27 % 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: 2.13 (0.21), residues: 664 sheet: 0.69 (0.17), residues: 952 loop : -1.04 (0.13), residues: 2109 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 36 HIS 0.003 0.001 HIS B1058 PHE 0.023 0.001 PHE C 559 TYR 0.019 0.001 TYR F 49 ARG 0.005 0.000 ARG G 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6471.39 seconds wall clock time: 120 minutes 46.18 seconds (7246.18 seconds total)