Starting phenix.real_space_refine on Thu Mar 21 13:49:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdb_33142/03_2024/7xdb_33142_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdb_33142/03_2024/7xdb_33142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.62 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdb_33142/03_2024/7xdb_33142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdb_33142/03_2024/7xdb_33142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdb_33142/03_2024/7xdb_33142_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xdb_33142/03_2024/7xdb_33142_neut.pdb" } resolution = 2.62 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.077 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 19301 2.51 5 N 4957 2.21 5 O 5799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 70": "OE1" <-> "OE2" Residue "E TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A GLU 868": "OE1" <-> "OE2" Residue "A PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 47": "OE1" <-> "OE2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C PHE 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 868": "OE1" <-> "OE2" Residue "C GLU 1072": "OE1" <-> "OE2" Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 309": "OE1" <-> "OE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 340": "OE1" <-> "OE2" Residue "B GLU 1072": "OE1" <-> "OE2" Residue "I TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30189 Number of models: 1 Model: "" Number of chains: 23 Chain: "E" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 8126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1034, 8126 Classifications: {'peptide': 1034} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 56, 'TRANS': 977} Chain breaks: 8 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 929 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "G" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 929 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} Chain: "F" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "C" Number of atoms: 8121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1033, 8121 Classifications: {'peptide': 1033} Link IDs: {'PTRANS': 56, 'TRANS': 976} Chain breaks: 8 Chain: "B" Number of atoms: 8169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8169 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 57, 'TRANS': 982} Chain breaks: 7 Chain: "H" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 818 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "I" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 929 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 5, 'TRANS': 112} 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: "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: "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: "Z" 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: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 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 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 14.56, per 1000 atoms: 0.48 Number of scatterers: 30189 At special positions: 0 Unit cell: (138.672, 171.2, 192.6, 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 5799 8.00 N 4957 7.00 C 19301 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 132 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 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=2.02 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 D 22 " - pdb=" SG CYS D 97 " distance=2.03 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 97 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 164 " 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=2.04 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=2.06 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=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 132 " - pdb=" SG CYS B 164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 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=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 97 " 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 O 1 " - " NAG O 2 " " NAG S 1 " - " NAG S 2 " " NAG U 1 " - " NAG U 2 " " NAG Z 1 " - " NAG Z 2 " " NAG d 1 " - " NAG d 2 " " NAG f 1 " - " NAG f 2 " " NAG i 1 " - " NAG i 2 " NAG-ASN " NAG A1201 " - " ASN A1134 " " NAG A1202 " - " ASN A 709 " " NAG A1203 " - " ASN A1074 " " NAG A1204 " - " ASN A 616 " " NAG B1201 " - " ASN B1134 " " NAG B1202 " - " ASN B 709 " " NAG B1203 " - " ASN B1074 " " NAG B1204 " - " ASN B 616 " " NAG B1205 " - " ASN B 234 " " NAG B1206 " - " ASN B 163 " " NAG B1207 " - " ASN B 64 " " NAG C1201 " - " ASN C1134 " " NAG C1202 " - " ASN C 709 " " NAG C1203 " - " ASN C1074 " " NAG C1204 " - " ASN C 616 " " NAG C1205 " - " ASN C 331 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A 717 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A 343 " " NAG O 1 " - " ASN C1098 " " NAG S 1 " - " ASN C 717 " " NAG U 1 " - " ASN C 801 " " NAG Z 1 " - " ASN B1098 " " NAG d 1 " - " ASN B 717 " " NAG f 1 " - " ASN B 801 " " NAG i 1 " - " ASN B 343 " Time building additional restraints: 12.20 Conformation dependent library (CDL) restraints added in 5.4 seconds 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7054 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 69 sheets defined 21.8% alpha, 32.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.97 Creating SS restraints... Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.590A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 371 removed outlier: 4.100A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 371 " --> pdb=" O VAL A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 365 through 371' Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.386A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.936A 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 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.728A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 783 Processing helix chain 'A' and resid 796 through 800 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.517A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 3.987A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.805A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.617A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.684A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 33 Processing helix chain 'G' and resid 29 through 33 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 371 removed outlier: 3.902A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU C 371 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 389 removed outlier: 4.085A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 630 through 635 removed outlier: 3.558A pdb=" N VAL C 635 " --> pdb=" O PRO C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 638 No H-bonds generated for 'chain 'C' and resid 636 through 638' Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 Processing helix chain 'C' and resid 796 through 800 Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.589A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 3.948A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 removed outlier: 3.694A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.683A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA C 958 " --> pdb=" O HIS C 954 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1032 removed outlier: 3.575A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.902A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 371 " --> pdb=" O LEU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.085A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 755 removed outlier: 3.992A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 Processing helix chain 'B' and resid 796 through 800 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 3.911A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 removed outlier: 3.856A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.624A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA B 958 " --> pdb=" O HIS B 954 " (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: 4.015A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 33 Processing sheet with id=AA1, first strand: chain 'E' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.542A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.542A pdb=" N LEU E 11 " --> pdb=" O GLU E 105 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 33 removed outlier: 4.186A pdb=" N ALA A 30 " --> pdb=" O TRP A 67 " (cutoff:3.500A) removed outlier: 8.585A pdb=" N ASN A 64 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N TYR A 269 " --> pdb=" O ASN A 64 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA A 264 " --> pdb=" O ILE A 96 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE A 199 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP A 228 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE A 201 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.007A pdb=" N PHE A 46 " --> pdb=" O ARG C 567 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 58 removed outlier: 3.936A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 85 through 86 removed outlier: 7.245A pdb=" N LEU A 142 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 85 through 86 removed outlier: 6.102A pdb=" N ALA A 243 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N ILE A 102 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 166 " --> pdb=" O VAL A 131 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.890A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.383A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AB3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.451A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB5, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.385A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.490A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.540A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.540A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.515A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 787 through 790 removed outlier: 5.584A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.484A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'D' and resid 58 through 61 removed outlier: 3.593A pdb=" N ILE D 51 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE D 51 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE D 35 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP D 34 " --> pdb=" O HIS D 100 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 58 through 61 removed outlier: 3.593A pdb=" N ILE D 51 " --> pdb=" O ARG D 60 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N TRP D 37 " --> pdb=" O MET D 49 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ILE D 51 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE D 35 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N TRP D 34 " --> pdb=" O HIS D 100 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AC8, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.813A pdb=" N THR G 118 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ILE G 35 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE G 51 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP G 37 " --> pdb=" O MET G 49 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP G 58 " --> pdb=" O TYR G 53 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 10 through 11 removed outlier: 3.813A pdb=" N THR G 118 " --> pdb=" O GLU G 10 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU G 110 " --> pdb=" O ARG G 99 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.651A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 10 through 12 Processing sheet with id=AD3, first strand: chain 'F' and resid 53 through 54 removed outlier: 6.493A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 30 through 33 removed outlier: 4.237A pdb=" N ALA C 30 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 8.572A pdb=" N ASN C 64 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N TYR C 269 " --> pdb=" O ASN C 64 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N SER C 203 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 39 through 40 removed outlier: 7.069A pdb=" N VAL C 39 " --> pdb=" O LEU C 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 45 through 46 removed outlier: 5.463A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 50 through 58 removed outlier: 3.516A pdb=" N ASP C 56 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 85 through 86 removed outlier: 6.067A pdb=" N ALA C 243 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE C 102 " --> pdb=" O ALA C 243 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 85 through 86 removed outlier: 3.540A pdb=" N LEU C 142 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 129 through 130 Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.128A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.681A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.424A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.918A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.513A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.444A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.444A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.442A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 787 through 790 removed outlier: 5.626A pdb=" N ILE C 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.521A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 31 through 33 removed outlier: 7.722A pdb=" N ASN B 64 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N TYR B 269 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N PHE B 199 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP B 228 " --> pdb=" O PHE B 199 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ILE B 201 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N HIS B 205 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N ALA B 222 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N VAL B 39 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 50 through 58 removed outlier: 3.998A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 85 through 86 Processing sheet with id=AF7, first strand: chain 'B' and resid 85 through 86 removed outlier: 3.614A pdb=" N GLY B 104 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ALA B 243 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ILE B 102 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE B 166 " --> pdb=" O VAL B 131 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 135 through 136 removed outlier: 6.951A pdb=" N GLN B 135 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 311 through 319 removed outlier: 7.146A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.680A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.594A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AG4, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.918A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.900A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.439A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.439A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.402A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.697A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'H' and resid 4 through 7 removed outlier: 3.650A pdb=" N GLU H 70 " --> pdb=" O SER H 67 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'H' and resid 10 through 12 Processing sheet with id=AH3, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.494A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'I' and resid 3 through 6 Processing sheet with id=AH5, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.814A pdb=" N THR I 118 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE I 35 " --> pdb=" O ILE I 51 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE I 51 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP I 37 " --> pdb=" O MET I 49 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP I 58 " --> pdb=" O TYR I 53 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'I' and resid 10 through 11 removed outlier: 3.814A pdb=" N THR I 118 " --> pdb=" O GLU I 10 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU I 110 " --> pdb=" O ARG I 99 " (cutoff:3.500A) 1299 hydrogen bonds defined for protein. 3462 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: 15.08 Time building geometry restraints manager: 13.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4972 1.32 - 1.45: 8857 1.45 - 1.58: 16924 1.58 - 1.70: 0 1.70 - 1.83: 168 Bond restraints: 30921 Sorted by residual: bond pdb=" C PRO C 986 " pdb=" O PRO C 986 " ideal model delta sigma weight residual 1.240 1.195 0.045 1.12e-02 7.97e+03 1.61e+01 bond pdb=" N VAL C 534 " pdb=" CA VAL C 534 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.22e-02 6.72e+03 9.63e+00 bond pdb=" N VAL C 327 " pdb=" CA VAL C 327 " ideal model delta sigma weight residual 1.459 1.495 -0.037 1.20e-02 6.94e+03 9.30e+00 bond pdb=" N THR C 581 " pdb=" CA THR C 581 " ideal model delta sigma weight residual 1.455 1.496 -0.040 1.33e-02 5.65e+03 9.27e+00 bond pdb=" N ILE C 332 " pdb=" CA ILE C 332 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.97e+00 ... (remaining 30916 not shown) Histogram of bond angle deviations from ideal: 96.52 - 104.06: 507 104.06 - 111.61: 14342 111.61 - 119.16: 10390 119.16 - 126.71: 16390 126.71 - 134.26: 427 Bond angle restraints: 42056 Sorted by residual: angle pdb=" N PRO C 986 " pdb=" CA PRO C 986 " pdb=" C PRO C 986 " ideal model delta sigma weight residual 110.70 117.99 -7.29 1.22e+00 6.72e-01 3.57e+01 angle pdb=" N GLY B 757 " pdb=" CA GLY B 757 " pdb=" C GLY B 757 " ideal model delta sigma weight residual 111.21 116.67 -5.46 1.04e+00 9.25e-01 2.76e+01 angle pdb=" CA PRO C 986 " pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 117.93 124.04 -6.11 1.20e+00 6.94e-01 2.59e+01 angle pdb=" C LYS C 528 " pdb=" N LYS C 529 " pdb=" CA LYS C 529 " ideal model delta sigma weight residual 122.95 115.93 7.02 1.44e+00 4.82e-01 2.38e+01 angle pdb=" CA LYS C 528 " pdb=" C LYS C 528 " pdb=" O LYS C 528 " ideal model delta sigma weight residual 121.94 116.37 5.57 1.15e+00 7.56e-01 2.34e+01 ... (remaining 42051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 17517 17.88 - 35.76: 1084 35.76 - 53.64: 188 53.64 - 71.52: 42 71.52 - 89.40: 24 Dihedral angle restraints: 18855 sinusoidal: 7871 harmonic: 10984 Sorted by residual: dihedral pdb=" CA CYS B 617 " pdb=" C CYS B 617 " pdb=" N THR B 618 " pdb=" CA THR B 618 " ideal model delta harmonic sigma weight residual 180.00 146.61 33.39 0 5.00e+00 4.00e-02 4.46e+01 dihedral pdb=" CB CYS B 617 " pdb=" SG CYS B 617 " pdb=" SG CYS B 649 " pdb=" CB CYS B 649 " ideal model delta sinusoidal sigma weight residual 93.00 47.06 45.94 1 1.00e+01 1.00e-02 2.92e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 97 " pdb=" CB CYS D 97 " ideal model delta sinusoidal sigma weight residual 93.00 49.18 43.82 1 1.00e+01 1.00e-02 2.67e+01 ... (remaining 18852 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.202: 4792 0.202 - 0.404: 13 0.404 - 0.606: 5 0.606 - 0.809: 0 0.809 - 1.011: 1 Chirality restraints: 4811 Sorted by residual: chirality pdb=" C1 NAG i 1 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG i 1 " pdb=" O5 NAG i 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.39 -1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" C1 NAG B1201 " pdb=" ND2 ASN B1134 " pdb=" C2 NAG B1201 " pdb=" O5 NAG B1201 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 8.07e+00 chirality pdb=" C1 NAG B1204 " pdb=" ND2 ASN B 616 " pdb=" C2 NAG B1204 " pdb=" O5 NAG B1204 " both_signs ideal model delta sigma weight residual False -2.40 -1.84 -0.56 2.00e-01 2.50e+01 7.90e+00 ... (remaining 4808 not shown) Planarity restraints: 5372 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1204 " -0.318 2.00e-02 2.50e+03 2.67e-01 8.94e+02 pdb=" C7 NAG C1204 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG C1204 " -0.192 2.00e-02 2.50e+03 pdb=" N2 NAG C1204 " 0.460 2.00e-02 2.50e+03 pdb=" O7 NAG C1204 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1205 " -0.274 2.00e-02 2.50e+03 2.30e-01 6.62e+02 pdb=" C7 NAG C1205 " 0.072 2.00e-02 2.50e+03 pdb=" C8 NAG C1205 " -0.181 2.00e-02 2.50e+03 pdb=" N2 NAG C1205 " 0.390 2.00e-02 2.50e+03 pdb=" O7 NAG C1205 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 229 " 0.052 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO A 230 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO A 230 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 230 " 0.043 5.00e-02 4.00e+02 ... (remaining 5369 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 391 2.67 - 3.23: 27920 3.23 - 3.78: 47794 3.78 - 4.34: 68833 4.34 - 4.90: 110813 Nonbonded interactions: 255751 Sorted by model distance: nonbonded pdb=" O PHE A 329 " pdb=" NE2 GLN A 580 " model vdw 2.111 2.520 nonbonded pdb=" OG SER E 63 " pdb=" OG1 THR E 74 " model vdw 2.132 2.440 nonbonded pdb=" OG1 THR B 110 " pdb=" OG1 THR B 115 " model vdw 2.150 2.440 nonbonded pdb=" O ASP B 81 " pdb=" OH TYR B 265 " model vdw 2.189 2.440 nonbonded pdb=" OG1 THR D 70 " pdb=" O GLN D 83 " model vdw 2.223 2.440 ... (remaining 255746 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' and (resid 29 through 620 or resid 629 through 827 or resid 848 throu \ gh 1144 or resid 1201 through 1204)) selection = (chain 'B' and (resid 29 through 620 or resid 629 through 1144 or resid 1201 thr \ ough 1204)) selection = (chain 'C' and (resid 29 through 827 or resid 848 through 1144 or resid 1201 thr \ ough 1204)) } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'S' selection = chain 'U' selection = chain 'Z' selection = chain 'd' selection = chain 'f' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 14.900 Check model and map are aligned: 0.430 Set scattering table: 0.240 Process input model: 81.260 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 30921 Z= 0.235 Angle : 0.638 7.478 42056 Z= 0.355 Chirality : 0.052 1.011 4811 Planarity : 0.007 0.267 5345 Dihedral : 12.333 89.397 11666 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.54 (0.13), residues: 3715 helix: 1.28 (0.20), residues: 734 sheet: 0.81 (0.15), residues: 1061 loop : -0.21 (0.13), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 886 HIS 0.012 0.001 HIS B 954 PHE 0.028 0.002 PHE C 906 TYR 0.043 0.002 TYR C 198 ARG 0.006 0.000 ARG B 765 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 373 time to evaluate : 3.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.8228 (ttpt) cc_final: 0.7922 (ptmt) REVERT: A 118 LEU cc_start: 0.6706 (mp) cc_final: 0.6444 (mt) REVERT: A 130 LYS cc_start: 0.8017 (mppt) cc_final: 0.7741 (mptt) REVERT: A 309 GLU cc_start: 0.7419 (mm-30) cc_final: 0.7148 (mm-30) REVERT: A 955 ASN cc_start: 0.7243 (t0) cc_final: 0.6774 (m110) REVERT: G 3 GLN cc_start: 0.7975 (mt0) cc_final: 0.7533 (pm20) REVERT: C 280 ASN cc_start: 0.7452 (p0) cc_final: 0.7222 (p0) REVERT: C 811 LYS cc_start: 0.6916 (mtmm) cc_final: 0.6196 (tptp) REVERT: B 100 ASN cc_start: 0.7921 (m-40) cc_final: 0.7578 (t0) REVERT: B 239 GLN cc_start: 0.7746 (tt0) cc_final: 0.7440 (tt0) REVERT: B 360 ASN cc_start: 0.8156 (m-40) cc_final: 0.7942 (m-40) REVERT: B 428 ASP cc_start: 0.7350 (p0) cc_final: 0.7101 (p0) REVERT: H 4 MET cc_start: 0.0444 (mmt) cc_final: -0.0385 (ttp) outliers start: 0 outliers final: 0 residues processed: 373 average time/residue: 1.2456 time to fit residues: 557.9273 Evaluate side-chains 268 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 314 optimal weight: 8.9990 chunk 282 optimal weight: 7.9990 chunk 156 optimal weight: 0.6980 chunk 96 optimal weight: 9.9990 chunk 190 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 chunk 292 optimal weight: 6.9990 chunk 113 optimal weight: 20.0000 chunk 177 optimal weight: 20.0000 chunk 217 optimal weight: 0.8980 chunk 338 optimal weight: 0.7980 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 3 GLN E 38 GLN E 79 GLN ** A 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN A 505 HIS A 779 GLN A 957 GLN D 40 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 ASN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 762 GLN C 907 ASN C1010 GLN C1125 ASN B 907 ASN B1010 GLN ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 6 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 30921 Z= 0.396 Angle : 0.637 9.353 42056 Z= 0.333 Chirality : 0.052 0.818 4811 Planarity : 0.005 0.064 5345 Dihedral : 6.371 58.825 4862 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.52 % Allowed : 7.09 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.32 (0.13), residues: 3715 helix: 1.25 (0.19), residues: 729 sheet: 0.64 (0.16), residues: 1019 loop : -0.38 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 886 HIS 0.005 0.001 HIS D 100 PHE 0.039 0.002 PHE C 906 TYR 0.035 0.002 TYR B 265 ARG 0.006 0.001 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 267 time to evaluate : 3.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.8296 (ttpt) cc_final: 0.8026 (ptmt) REVERT: A 309 GLU cc_start: 0.7519 (mm-30) cc_final: 0.7167 (mm-30) REVERT: A 326 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7993 (mp) REVERT: A 339 ASP cc_start: 0.8030 (t70) cc_final: 0.7584 (t0) REVERT: A 580 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.6645 (mp10) REVERT: D 3 GLN cc_start: 0.7901 (pm20) cc_final: 0.7661 (pm20) REVERT: D 21 SER cc_start: 0.8159 (OUTLIER) cc_final: 0.7939 (t) REVERT: D 37 TRP cc_start: 0.7933 (m100) cc_final: 0.6926 (m100) REVERT: D 60 ARG cc_start: 0.8416 (ttm170) cc_final: 0.8214 (ttm-80) REVERT: D 96 TYR cc_start: 0.8297 (m-80) cc_final: 0.7781 (m-10) REVERT: G 94 MET cc_start: 0.6889 (tmm) cc_final: 0.6589 (tpp) REVERT: C 675 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.6769 (mp10) REVERT: C 811 LYS cc_start: 0.6817 (mtmm) cc_final: 0.6348 (tptp) REVERT: B 100 ASN cc_start: 0.7774 (m-40) cc_final: 0.7388 (t0) REVERT: B 360 ASN cc_start: 0.8196 (m-40) cc_final: 0.7935 (m-40) REVERT: B 428 ASP cc_start: 0.7406 (p0) cc_final: 0.7201 (p0) REVERT: B 957 GLN cc_start: 0.7810 (tt0) cc_final: 0.7566 (tt0) REVERT: H 4 MET cc_start: 0.0625 (mmt) cc_final: -0.0332 (ttp) outliers start: 50 outliers final: 22 residues processed: 303 average time/residue: 1.2422 time to fit residues: 454.0670 Evaluate side-chains 269 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 243 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 188 optimal weight: 6.9990 chunk 105 optimal weight: 0.9980 chunk 281 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 339 optimal weight: 0.5980 chunk 366 optimal weight: 20.0000 chunk 302 optimal weight: 0.9990 chunk 336 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 272 optimal weight: 0.0970 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 417 ASN A 779 GLN A 895 GLN A 957 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN F 38 GLN ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 957 GLN C1125 ASN B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30921 Z= 0.190 Angle : 0.527 9.498 42056 Z= 0.274 Chirality : 0.046 0.742 4811 Planarity : 0.004 0.048 5345 Dihedral : 5.932 59.308 4862 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.58 % Allowed : 8.94 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.41 (0.13), residues: 3715 helix: 1.57 (0.19), residues: 722 sheet: 0.64 (0.16), residues: 1009 loop : -0.37 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 96 HIS 0.005 0.001 HIS A 69 PHE 0.024 0.001 PHE C 166 TYR 0.028 0.001 TYR B 265 ARG 0.004 0.000 ARG B 646 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 276 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.8275 (ttpt) cc_final: 0.8045 (ptmt) REVERT: A 233 ILE cc_start: 0.7164 (OUTLIER) cc_final: 0.6887 (tp) REVERT: A 309 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7169 (mm-30) REVERT: A 326 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7893 (mp) REVERT: A 339 ASP cc_start: 0.8035 (t70) cc_final: 0.7609 (t0) REVERT: A 357 ARG cc_start: 0.8173 (ttt-90) cc_final: 0.7878 (ttt-90) REVERT: A 1038 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7734 (mmtt) REVERT: D 3 GLN cc_start: 0.7932 (pm20) cc_final: 0.7636 (pm20) REVERT: D 37 TRP cc_start: 0.8054 (m100) cc_final: 0.7432 (m100) REVERT: D 41 MET cc_start: 0.7781 (tpt) cc_final: 0.7524 (mmm) REVERT: D 49 MET cc_start: 0.8491 (mtp) cc_final: 0.8111 (mtm) REVERT: D 60 ARG cc_start: 0.8435 (ttm170) cc_final: 0.8227 (ttm-80) REVERT: G 49 MET cc_start: 0.8042 (mtm) cc_final: 0.7770 (mtp) REVERT: G 94 MET cc_start: 0.6848 (tmm) cc_final: 0.6483 (tpp) REVERT: C 239 GLN cc_start: 0.6453 (tt0) cc_final: 0.5941 (mm-40) REVERT: C 633 TRP cc_start: 0.5496 (m100) cc_final: 0.5270 (m100) REVERT: C 675 GLN cc_start: 0.7610 (OUTLIER) cc_final: 0.6784 (mp10) REVERT: C 811 LYS cc_start: 0.6799 (mtmm) cc_final: 0.6333 (tptp) REVERT: C 988 GLU cc_start: 0.7398 (mp0) cc_final: 0.6900 (tp30) REVERT: B 100 ASN cc_start: 0.7727 (m-40) cc_final: 0.7443 (t0) REVERT: B 360 ASN cc_start: 0.8170 (m-40) cc_final: 0.7934 (m-40) REVERT: B 760 CYS cc_start: 0.4909 (OUTLIER) cc_final: 0.4479 (m) REVERT: B 957 GLN cc_start: 0.7765 (tt0) cc_final: 0.7528 (tt0) REVERT: H 4 MET cc_start: 0.0379 (mmt) cc_final: -0.0718 (ptp) outliers start: 52 outliers final: 20 residues processed: 308 average time/residue: 1.1767 time to fit residues: 439.9903 Evaluate side-chains 278 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 253 time to evaluate : 3.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 760 CYS Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 335 optimal weight: 4.9990 chunk 255 optimal weight: 10.0000 chunk 176 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 161 optimal weight: 7.9990 chunk 227 optimal weight: 5.9990 chunk 340 optimal weight: 0.7980 chunk 360 optimal weight: 40.0000 chunk 177 optimal weight: 20.0000 chunk 322 optimal weight: 5.9990 chunk 97 optimal weight: 0.0570 overall best weight: 3.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 3 GLN A 417 ASN A 895 GLN A 957 GLN ** D 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN B 505 HIS ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 30921 Z= 0.504 Angle : 0.659 9.701 42056 Z= 0.343 Chirality : 0.053 0.906 4811 Planarity : 0.005 0.072 5345 Dihedral : 6.087 58.582 4862 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.39 % Allowed : 9.91 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.00 (0.13), residues: 3715 helix: 0.99 (0.19), residues: 718 sheet: 0.44 (0.16), residues: 1002 loop : -0.57 (0.13), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 886 HIS 0.010 0.001 HIS D 100 PHE 0.021 0.002 PHE A 898 TYR 0.033 0.002 TYR B 265 ARG 0.005 0.001 ARG C1000 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 259 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.8257 (ttpt) cc_final: 0.7952 (ptmt) REVERT: A 103 ARG cc_start: 0.6997 (mtt180) cc_final: 0.6445 (mmt90) REVERT: A 233 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.7099 (tp) REVERT: A 339 ASP cc_start: 0.8023 (t70) cc_final: 0.7604 (t0) REVERT: A 561 PRO cc_start: 0.8691 (Cg_exo) cc_final: 0.8365 (Cg_endo) REVERT: A 580 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.6623 (mp10) REVERT: A 1038 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7769 (mmtt) REVERT: D 3 GLN cc_start: 0.7973 (pm20) cc_final: 0.7636 (pm20) REVERT: D 21 SER cc_start: 0.8239 (OUTLIER) cc_final: 0.8013 (t) REVERT: D 37 TRP cc_start: 0.8081 (m100) cc_final: 0.7384 (m100) REVERT: D 49 MET cc_start: 0.8523 (mtp) cc_final: 0.8064 (mtm) REVERT: D 97 CYS cc_start: 0.7522 (t) cc_final: 0.7029 (t) REVERT: G 3 GLN cc_start: 0.7980 (mt0) cc_final: 0.7637 (pt0) REVERT: G 49 MET cc_start: 0.8188 (mtm) cc_final: 0.7869 (mtp) REVERT: G 94 MET cc_start: 0.6815 (OUTLIER) cc_final: 0.6312 (tpp) REVERT: G 96 TYR cc_start: 0.8282 (m-80) cc_final: 0.7897 (m-80) REVERT: F 37 GLN cc_start: 0.6595 (OUTLIER) cc_final: 0.5463 (tp-100) REVERT: C 239 GLN cc_start: 0.6494 (tt0) cc_final: 0.5846 (mm-40) REVERT: C 675 GLN cc_start: 0.7705 (OUTLIER) cc_final: 0.6552 (mp10) REVERT: C 729 VAL cc_start: 0.9012 (OUTLIER) cc_final: 0.8762 (t) REVERT: C 811 LYS cc_start: 0.6940 (mtmm) cc_final: 0.6403 (tptp) REVERT: B 44 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.6957 (mptp) REVERT: B 100 ASN cc_start: 0.7873 (m-40) cc_final: 0.7389 (t0) REVERT: B 360 ASN cc_start: 0.8210 (m-40) cc_final: 0.7960 (m-40) REVERT: B 529 LYS cc_start: 0.8251 (OUTLIER) cc_final: 0.7684 (mmtt) REVERT: B 646 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7792 (mtp180) REVERT: B 814 LYS cc_start: 0.7993 (mptm) cc_final: 0.7664 (mtpt) REVERT: B 957 GLN cc_start: 0.7789 (tt0) cc_final: 0.7566 (tt0) REVERT: H 4 MET cc_start: 0.0364 (mmt) cc_final: -0.0710 (ptp) outliers start: 79 outliers final: 37 residues processed: 313 average time/residue: 1.1858 time to fit residues: 450.6690 Evaluate side-chains 295 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 247 time to evaluate : 3.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 37 GLN Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 729 VAL Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain B residue 44 LYS Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 503 VAL Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain B residue 1136 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 300 optimal weight: 4.9990 chunk 204 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 268 optimal weight: 1.9990 chunk 148 optimal weight: 0.9990 chunk 307 optimal weight: 0.9980 chunk 249 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 323 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 957 GLN D 83 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 505 HIS ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 30921 Z= 0.207 Angle : 0.535 12.446 42056 Z= 0.277 Chirality : 0.047 0.784 4811 Planarity : 0.004 0.046 5345 Dihedral : 5.655 59.835 4862 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.00 % Allowed : 11.55 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.13), residues: 3715 helix: 1.38 (0.20), residues: 719 sheet: 0.54 (0.16), residues: 996 loop : -0.50 (0.13), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP F 96 HIS 0.006 0.001 HIS D 100 PHE 0.029 0.001 PHE C 166 TYR 0.036 0.001 TYR D 96 ARG 0.003 0.000 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 266 time to evaluate : 3.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.8192 (ttpt) cc_final: 0.7938 (ptmt) REVERT: A 130 LYS cc_start: 0.7619 (mtmm) cc_final: 0.7275 (mptt) REVERT: A 233 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.7069 (tp) REVERT: A 335 LEU cc_start: 0.8949 (mp) cc_final: 0.8718 (mp) REVERT: A 339 ASP cc_start: 0.8022 (t70) cc_final: 0.7609 (t0) REVERT: A 561 PRO cc_start: 0.8677 (Cg_exo) cc_final: 0.8392 (Cg_endo) REVERT: A 580 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.6544 (mp10) REVERT: A 675 GLN cc_start: 0.7318 (mm110) cc_final: 0.7063 (tp40) REVERT: A 1038 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7915 (mmtt) REVERT: D 3 GLN cc_start: 0.7951 (pm20) cc_final: 0.7591 (pm20) REVERT: D 37 TRP cc_start: 0.8162 (m100) cc_final: 0.7425 (m100) REVERT: D 49 MET cc_start: 0.8489 (mtp) cc_final: 0.7988 (mtm) REVERT: D 97 CYS cc_start: 0.7353 (t) cc_final: 0.6802 (t) REVERT: G 3 GLN cc_start: 0.8007 (mt0) cc_final: 0.7665 (pt0) REVERT: G 19 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7088 (tptm) REVERT: G 49 MET cc_start: 0.8118 (mtm) cc_final: 0.7870 (mtp) REVERT: G 83 GLN cc_start: 0.6633 (OUTLIER) cc_final: 0.6170 (tm-30) REVERT: G 94 MET cc_start: 0.6914 (OUTLIER) cc_final: 0.6468 (tpp) REVERT: G 96 TYR cc_start: 0.8274 (m-80) cc_final: 0.7845 (m-80) REVERT: C 239 GLN cc_start: 0.6427 (tt0) cc_final: 0.5822 (mm-40) REVERT: C 613 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8145 (mt0) REVERT: C 675 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.6643 (mp10) REVERT: C 811 LYS cc_start: 0.6863 (mtmm) cc_final: 0.6366 (tptp) REVERT: B 100 ASN cc_start: 0.7747 (m-40) cc_final: 0.7306 (t0) REVERT: B 360 ASN cc_start: 0.8186 (m-40) cc_final: 0.7948 (m-40) REVERT: B 529 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7696 (mmtt) REVERT: B 654 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7851 (tm-30) REVERT: B 814 LYS cc_start: 0.7935 (mptm) cc_final: 0.7601 (mtpt) REVERT: B 957 GLN cc_start: 0.7789 (tt0) cc_final: 0.7546 (tt0) REVERT: B 1001 LEU cc_start: 0.8863 (tp) cc_final: 0.8618 (mt) REVERT: H 4 MET cc_start: 0.0156 (mmt) cc_final: -0.0434 (ptp) outliers start: 66 outliers final: 29 residues processed: 310 average time/residue: 1.1706 time to fit residues: 443.5098 Evaluate side-chains 290 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 251 time to evaluate : 3.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain G residue 19 LYS Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 121 optimal weight: 0.0870 chunk 324 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 211 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 360 optimal weight: 5.9990 chunk 299 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 189 optimal weight: 20.0000 overall best weight: 1.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 417 ASN A 779 GLN A 957 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 30921 Z= 0.209 Angle : 0.530 13.448 42056 Z= 0.274 Chirality : 0.046 0.743 4811 Planarity : 0.004 0.048 5345 Dihedral : 5.445 59.352 4862 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.00 % Allowed : 11.97 % Favored : 86.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.13), residues: 3715 helix: 1.50 (0.20), residues: 720 sheet: 0.57 (0.16), residues: 990 loop : -0.50 (0.13), residues: 2005 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP F 96 HIS 0.005 0.001 HIS D 100 PHE 0.038 0.001 PHE A 35 TYR 0.036 0.001 TYR D 96 ARG 0.003 0.000 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 263 time to evaluate : 3.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.8184 (ttpt) cc_final: 0.7932 (ptmt) REVERT: A 130 LYS cc_start: 0.7661 (mtmm) cc_final: 0.7280 (mptt) REVERT: A 233 ILE cc_start: 0.7354 (OUTLIER) cc_final: 0.7031 (tp) REVERT: A 335 LEU cc_start: 0.8944 (mp) cc_final: 0.8719 (mp) REVERT: A 339 ASP cc_start: 0.8006 (t70) cc_final: 0.7590 (t0) REVERT: A 561 PRO cc_start: 0.8645 (Cg_exo) cc_final: 0.8379 (Cg_endo) REVERT: A 580 GLN cc_start: 0.8635 (OUTLIER) cc_final: 0.6514 (mp10) REVERT: A 1038 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7896 (mmtt) REVERT: D 3 GLN cc_start: 0.7999 (pm20) cc_final: 0.7629 (pm20) REVERT: D 37 TRP cc_start: 0.8162 (m100) cc_final: 0.7439 (m100) REVERT: D 49 MET cc_start: 0.8506 (mtp) cc_final: 0.8019 (mtm) REVERT: D 97 CYS cc_start: 0.7217 (t) cc_final: 0.6654 (t) REVERT: G 3 GLN cc_start: 0.8018 (mt0) cc_final: 0.7664 (pt0) REVERT: G 19 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7452 (tptp) REVERT: G 49 MET cc_start: 0.8255 (mtm) cc_final: 0.7931 (mtp) REVERT: G 83 GLN cc_start: 0.6598 (OUTLIER) cc_final: 0.5710 (tm-30) REVERT: G 94 MET cc_start: 0.6908 (OUTLIER) cc_final: 0.6458 (tpp) REVERT: G 96 TYR cc_start: 0.8254 (m-80) cc_final: 0.7871 (m-80) REVERT: C 239 GLN cc_start: 0.6411 (tt0) cc_final: 0.5774 (mm-40) REVERT: C 309 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7587 (mm-30) REVERT: C 613 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8095 (mt0) REVERT: C 675 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.6715 (mp10) REVERT: C 811 LYS cc_start: 0.6946 (mtmm) cc_final: 0.6360 (tptp) REVERT: B 100 ASN cc_start: 0.7748 (m-40) cc_final: 0.7260 (t0) REVERT: B 360 ASN cc_start: 0.8179 (m-40) cc_final: 0.7938 (m-40) REVERT: B 421 TYR cc_start: 0.7051 (m-10) cc_final: 0.6596 (m-10) REVERT: B 465 GLU cc_start: 0.6894 (tp30) cc_final: 0.6670 (tp30) REVERT: B 529 LYS cc_start: 0.8263 (OUTLIER) cc_final: 0.7711 (mmtt) REVERT: B 646 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7743 (mtp180) REVERT: B 654 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7883 (tm-30) REVERT: B 814 LYS cc_start: 0.7923 (mptm) cc_final: 0.7583 (mtpt) REVERT: B 957 GLN cc_start: 0.7797 (tt0) cc_final: 0.7568 (tt0) REVERT: B 1001 LEU cc_start: 0.8849 (tp) cc_final: 0.8606 (mt) REVERT: H 4 MET cc_start: 0.0373 (mmt) cc_final: -0.0361 (ptp) outliers start: 66 outliers final: 34 residues processed: 310 average time/residue: 1.2099 time to fit residues: 458.1076 Evaluate side-chains 299 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 253 time to evaluate : 3.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 849 LEU Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain G residue 19 LYS Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 849 LEU Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain I residue 69 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 347 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 205 optimal weight: 0.0980 chunk 263 optimal weight: 0.4980 chunk 204 optimal weight: 1.9990 chunk 303 optimal weight: 7.9990 chunk 201 optimal weight: 0.6980 chunk 359 optimal weight: 5.9990 chunk 224 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 218 GLN A 417 ASN A 957 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 30921 Z= 0.174 Angle : 0.513 11.083 42056 Z= 0.265 Chirality : 0.046 0.712 4811 Planarity : 0.004 0.048 5345 Dihedral : 5.288 59.181 4862 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.85 % Allowed : 12.49 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.33 (0.13), residues: 3715 helix: 1.64 (0.20), residues: 718 sheet: 0.62 (0.16), residues: 995 loop : -0.50 (0.13), residues: 2002 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP F 96 HIS 0.004 0.001 HIS D 100 PHE 0.029 0.001 PHE C 166 TYR 0.035 0.001 TYR D 96 ARG 0.004 0.000 ARG I 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 263 time to evaluate : 3.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.8183 (ttpt) cc_final: 0.7955 (ptmt) REVERT: E 94 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7753 (t80) REVERT: A 130 LYS cc_start: 0.7605 (mtmm) cc_final: 0.7269 (mptt) REVERT: A 233 ILE cc_start: 0.7309 (OUTLIER) cc_final: 0.6976 (tp) REVERT: A 335 LEU cc_start: 0.8955 (mp) cc_final: 0.8732 (mp) REVERT: A 339 ASP cc_start: 0.8014 (t70) cc_final: 0.7599 (t0) REVERT: A 960 ASN cc_start: 0.8058 (m-40) cc_final: 0.7751 (t0) REVERT: A 1017 GLU cc_start: 0.7773 (tt0) cc_final: 0.7538 (tt0) REVERT: A 1038 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7913 (mmtt) REVERT: D 3 GLN cc_start: 0.7987 (pm20) cc_final: 0.7585 (pm20) REVERT: D 37 TRP cc_start: 0.8196 (m100) cc_final: 0.7499 (m100) REVERT: D 49 MET cc_start: 0.8420 (mtp) cc_final: 0.7977 (mtm) REVERT: D 97 CYS cc_start: 0.7181 (t) cc_final: 0.6636 (t) REVERT: G 3 GLN cc_start: 0.8028 (mt0) cc_final: 0.7663 (pt0) REVERT: G 49 MET cc_start: 0.8244 (mtm) cc_final: 0.7957 (mtp) REVERT: G 83 GLN cc_start: 0.6628 (OUTLIER) cc_final: 0.5827 (tm-30) REVERT: G 94 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6477 (tpp) REVERT: G 96 TYR cc_start: 0.8283 (m-80) cc_final: 0.7946 (m-80) REVERT: C 239 GLN cc_start: 0.6371 (tt0) cc_final: 0.5782 (mp10) REVERT: C 309 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7599 (mm-30) REVERT: C 675 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.6752 (mp10) REVERT: C 811 LYS cc_start: 0.6924 (mtmm) cc_final: 0.6317 (tptp) REVERT: B 100 ASN cc_start: 0.7744 (m-40) cc_final: 0.7256 (t0) REVERT: B 360 ASN cc_start: 0.8161 (m-40) cc_final: 0.7927 (m-40) REVERT: B 421 TYR cc_start: 0.7076 (m-10) cc_final: 0.6575 (m-10) REVERT: B 465 GLU cc_start: 0.6857 (tp30) cc_final: 0.6649 (tp30) REVERT: B 529 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7712 (mmtt) REVERT: B 654 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7909 (tm-30) REVERT: B 957 GLN cc_start: 0.7794 (tt0) cc_final: 0.7564 (tt0) REVERT: H 4 MET cc_start: 0.0450 (mmt) cc_final: -0.0343 (ptp) REVERT: I 49 MET cc_start: 0.0700 (mtp) cc_final: 0.0316 (mmm) outliers start: 61 outliers final: 34 residues processed: 302 average time/residue: 1.1659 time to fit residues: 433.7758 Evaluate side-chains 296 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 253 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 83 GLN Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 661 GLU Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain H residue 14 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 222 optimal weight: 2.9990 chunk 143 optimal weight: 8.9990 chunk 214 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 70 optimal weight: 0.0060 chunk 69 optimal weight: 1.9990 chunk 228 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 177 optimal weight: 30.0000 chunk 33 optimal weight: 1.9990 chunk 282 optimal weight: 9.9990 overall best weight: 1.1000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 GLN A 957 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 116 GLN ** H 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 30921 Z= 0.201 Angle : 0.518 9.880 42056 Z= 0.267 Chirality : 0.046 0.711 4811 Planarity : 0.004 0.048 5345 Dihedral : 5.219 58.198 4862 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.76 % Allowed : 12.73 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.33 (0.13), residues: 3715 helix: 1.64 (0.20), residues: 718 sheet: 0.61 (0.16), residues: 998 loop : -0.49 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP F 96 HIS 0.004 0.001 HIS D 100 PHE 0.028 0.001 PHE C 166 TYR 0.036 0.001 TYR D 96 ARG 0.003 0.000 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 259 time to evaluate : 3.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.8176 (ttpt) cc_final: 0.7955 (ptmt) REVERT: E 94 PHE cc_start: 0.8452 (OUTLIER) cc_final: 0.7773 (t80) REVERT: A 103 ARG cc_start: 0.6837 (mtt180) cc_final: 0.6304 (mmt90) REVERT: A 130 LYS cc_start: 0.7615 (mtmm) cc_final: 0.7275 (mptt) REVERT: A 335 LEU cc_start: 0.8963 (mp) cc_final: 0.8746 (mp) REVERT: A 339 ASP cc_start: 0.8016 (t70) cc_final: 0.7603 (t0) REVERT: A 357 ARG cc_start: 0.8186 (ttt-90) cc_final: 0.7884 (ttt-90) REVERT: A 580 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.6506 (mp10) REVERT: A 960 ASN cc_start: 0.8124 (m-40) cc_final: 0.7752 (t0) REVERT: A 1038 LYS cc_start: 0.8340 (OUTLIER) cc_final: 0.7872 (mmtt) REVERT: D 3 GLN cc_start: 0.7976 (pm20) cc_final: 0.7576 (pm20) REVERT: D 37 TRP cc_start: 0.8214 (m100) cc_final: 0.7493 (m100) REVERT: D 49 MET cc_start: 0.8424 (mtp) cc_final: 0.7944 (mtm) REVERT: D 97 CYS cc_start: 0.7139 (t) cc_final: 0.6638 (t) REVERT: G 3 GLN cc_start: 0.8048 (mt0) cc_final: 0.7679 (pt0) REVERT: G 49 MET cc_start: 0.8266 (mtm) cc_final: 0.7946 (mtp) REVERT: G 94 MET cc_start: 0.6912 (OUTLIER) cc_final: 0.6460 (tpp) REVERT: G 96 TYR cc_start: 0.8312 (m-80) cc_final: 0.7997 (m-80) REVERT: C 198 TYR cc_start: 0.4415 (OUTLIER) cc_final: 0.3473 (t80) REVERT: C 239 GLN cc_start: 0.6392 (tt0) cc_final: 0.5808 (mp-120) REVERT: C 309 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7596 (mm-30) REVERT: C 613 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: B 100 ASN cc_start: 0.7743 (m-40) cc_final: 0.7227 (p0) REVERT: B 109 THR cc_start: 0.7474 (OUTLIER) cc_final: 0.7236 (m) REVERT: B 360 ASN cc_start: 0.8160 (m-40) cc_final: 0.7923 (m-40) REVERT: B 421 TYR cc_start: 0.7042 (m-10) cc_final: 0.6539 (m-10) REVERT: B 465 GLU cc_start: 0.6847 (tp30) cc_final: 0.6644 (tp30) REVERT: B 529 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7700 (mmtt) REVERT: B 646 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7645 (mtp180) REVERT: B 654 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7917 (tm-30) REVERT: B 957 GLN cc_start: 0.7792 (tt0) cc_final: 0.7559 (tt0) REVERT: H 4 MET cc_start: 0.0467 (mmt) cc_final: -0.0347 (ptp) REVERT: I 49 MET cc_start: 0.0662 (mtp) cc_final: 0.0283 (mmm) outliers start: 58 outliers final: 34 residues processed: 298 average time/residue: 1.1937 time to fit residues: 432.4812 Evaluate side-chains 298 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 253 time to evaluate : 3.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 60 ARG Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 849 LEU Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain I residue 69 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 327 optimal weight: 0.9980 chunk 344 optimal weight: 1.9990 chunk 314 optimal weight: 7.9990 chunk 335 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 145 optimal weight: 10.0000 chunk 263 optimal weight: 0.7980 chunk 102 optimal weight: 0.9990 chunk 302 optimal weight: 1.9990 chunk 316 optimal weight: 0.9980 chunk 333 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 218 GLN A 779 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30921 Z= 0.182 Angle : 0.511 9.797 42056 Z= 0.264 Chirality : 0.045 0.699 4811 Planarity : 0.004 0.050 5345 Dihedral : 5.174 58.210 4862 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.79 % Allowed : 12.91 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.31 (0.13), residues: 3715 helix: 1.69 (0.20), residues: 716 sheet: 0.58 (0.16), residues: 1002 loop : -0.51 (0.13), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP F 96 HIS 0.004 0.001 HIS D 100 PHE 0.028 0.001 PHE C 166 TYR 0.037 0.001 TYR D 96 ARG 0.004 0.000 ARG F 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 261 time to evaluate : 3.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.8176 (ttpt) cc_final: 0.7944 (ptmt) REVERT: E 94 PHE cc_start: 0.8441 (OUTLIER) cc_final: 0.7757 (t80) REVERT: A 103 ARG cc_start: 0.6796 (mtt180) cc_final: 0.6262 (mmt90) REVERT: A 130 LYS cc_start: 0.7594 (mtmm) cc_final: 0.7245 (mptt) REVERT: A 335 LEU cc_start: 0.8964 (mp) cc_final: 0.8750 (mp) REVERT: A 339 ASP cc_start: 0.8015 (t70) cc_final: 0.7601 (t0) REVERT: A 580 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.6495 (mp10) REVERT: A 960 ASN cc_start: 0.8129 (OUTLIER) cc_final: 0.7737 (t0) REVERT: A 1017 GLU cc_start: 0.7764 (tt0) cc_final: 0.7537 (tt0) REVERT: A 1038 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7996 (mmtt) REVERT: D 3 GLN cc_start: 0.7982 (pm20) cc_final: 0.7607 (pm20) REVERT: D 37 TRP cc_start: 0.8209 (m100) cc_final: 0.7849 (m100) REVERT: D 49 MET cc_start: 0.8414 (mtp) cc_final: 0.8017 (mtm) REVERT: D 97 CYS cc_start: 0.7157 (t) cc_final: 0.6693 (t) REVERT: G 3 GLN cc_start: 0.8047 (mt0) cc_final: 0.7692 (pt0) REVERT: G 49 MET cc_start: 0.8164 (mtm) cc_final: 0.7931 (mtp) REVERT: G 81 TYR cc_start: 0.7875 (m-80) cc_final: 0.7613 (m-10) REVERT: G 94 MET cc_start: 0.6918 (OUTLIER) cc_final: 0.6454 (tpp) REVERT: G 96 TYR cc_start: 0.8288 (m-80) cc_final: 0.7977 (m-80) REVERT: F 4 MET cc_start: 0.7375 (mtp) cc_final: 0.7147 (ttt) REVERT: C 198 TYR cc_start: 0.4419 (OUTLIER) cc_final: 0.3446 (t80) REVERT: C 239 GLN cc_start: 0.6383 (tt0) cc_final: 0.5800 (mp10) REVERT: C 309 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7598 (mm-30) REVERT: C 613 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8083 (mt0) REVERT: C 988 GLU cc_start: 0.7418 (mp0) cc_final: 0.6820 (tp30) REVERT: B 100 ASN cc_start: 0.7657 (m-40) cc_final: 0.7169 (p0) REVERT: B 109 THR cc_start: 0.7463 (OUTLIER) cc_final: 0.7220 (m) REVERT: B 360 ASN cc_start: 0.8172 (m-40) cc_final: 0.7939 (m-40) REVERT: B 529 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7696 (mmtt) REVERT: B 646 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.7660 (mtp180) REVERT: B 654 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7929 (tm-30) REVERT: B 957 GLN cc_start: 0.7798 (tt0) cc_final: 0.7562 (tt0) REVERT: H 4 MET cc_start: 0.0565 (mmt) cc_final: -0.0302 (ptp) outliers start: 59 outliers final: 33 residues processed: 301 average time/residue: 1.1900 time to fit residues: 438.4008 Evaluate side-chains 300 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 255 time to evaluate : 3.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 960 ASN Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1134 ASN Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain I residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 219 optimal weight: 1.9990 chunk 354 optimal weight: 30.0000 chunk 216 optimal weight: 2.9990 chunk 168 optimal weight: 0.9980 chunk 246 optimal weight: 2.9990 chunk 371 optimal weight: 7.9990 chunk 342 optimal weight: 0.9980 chunk 295 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 228 optimal weight: 5.9990 chunk 181 optimal weight: 30.0000 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 116 GLN A 218 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1010 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 30921 Z= 0.304 Angle : 0.558 9.354 42056 Z= 0.289 Chirality : 0.048 0.760 4811 Planarity : 0.004 0.050 5345 Dihedral : 5.277 57.442 4862 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.52 % Allowed : 13.37 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.13), residues: 3715 helix: 1.45 (0.19), residues: 718 sheet: 0.50 (0.16), residues: 1004 loop : -0.52 (0.13), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP F 96 HIS 0.007 0.001 HIS D 100 PHE 0.034 0.002 PHE B 562 TYR 0.037 0.002 TYR D 96 ARG 0.004 0.000 ARG B 567 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7430 Ramachandran restraints generated. 3715 Oldfield, 0 Emsley, 3715 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 255 time to evaluate : 3.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 45 LYS cc_start: 0.8166 (ttpt) cc_final: 0.7925 (ptmt) REVERT: E 94 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.7864 (t80) REVERT: A 103 ARG cc_start: 0.6857 (mtt180) cc_final: 0.6350 (mmt90) REVERT: A 130 LYS cc_start: 0.7635 (mtmm) cc_final: 0.7307 (mptp) REVERT: A 335 LEU cc_start: 0.8980 (mp) cc_final: 0.8767 (mp) REVERT: A 339 ASP cc_start: 0.8039 (t70) cc_final: 0.7619 (t0) REVERT: A 357 ARG cc_start: 0.8205 (ttt-90) cc_final: 0.8002 (ttt-90) REVERT: A 561 PRO cc_start: 0.8693 (Cg_exo) cc_final: 0.8410 (Cg_endo) REVERT: A 580 GLN cc_start: 0.8666 (OUTLIER) cc_final: 0.6599 (mp10) REVERT: A 1038 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7981 (mmtt) REVERT: D 3 GLN cc_start: 0.7998 (pm20) cc_final: 0.7621 (pm20) REVERT: D 37 TRP cc_start: 0.8229 (m100) cc_final: 0.7543 (m100) REVERT: D 49 MET cc_start: 0.8432 (mtp) cc_final: 0.7942 (mtm) REVERT: D 97 CYS cc_start: 0.7263 (t) cc_final: 0.6733 (t) REVERT: G 3 GLN cc_start: 0.8044 (mt0) cc_final: 0.7680 (pt0) REVERT: G 49 MET cc_start: 0.8233 (mtm) cc_final: 0.7876 (mtp) REVERT: G 81 TYR cc_start: 0.7933 (m-80) cc_final: 0.7640 (m-10) REVERT: G 94 MET cc_start: 0.6862 (OUTLIER) cc_final: 0.6361 (tpp) REVERT: G 96 TYR cc_start: 0.8317 (m-80) cc_final: 0.8083 (m-80) REVERT: C 198 TYR cc_start: 0.4529 (OUTLIER) cc_final: 0.3535 (t80) REVERT: C 239 GLN cc_start: 0.6463 (tt0) cc_final: 0.5818 (mp10) REVERT: C 309 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7587 (mm-30) REVERT: C 613 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8120 (mt0) REVERT: B 100 ASN cc_start: 0.7696 (m-40) cc_final: 0.7200 (p0) REVERT: B 109 THR cc_start: 0.7533 (OUTLIER) cc_final: 0.7259 (m) REVERT: B 360 ASN cc_start: 0.8209 (m-40) cc_final: 0.7959 (m-40) REVERT: B 421 TYR cc_start: 0.7094 (m-10) cc_final: 0.6751 (m-10) REVERT: B 529 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7701 (mmtt) REVERT: B 646 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7743 (mtp180) REVERT: B 654 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7887 (tm-30) REVERT: B 814 LYS cc_start: 0.7928 (mptm) cc_final: 0.7594 (mtpt) REVERT: B 957 GLN cc_start: 0.7804 (tt0) cc_final: 0.7560 (tt0) REVERT: H 4 MET cc_start: 0.0533 (mmt) cc_final: -0.0361 (ptp) REVERT: I 41 MET cc_start: 0.3330 (ptp) cc_final: 0.2640 (mmp) outliers start: 50 outliers final: 35 residues processed: 288 average time/residue: 1.1640 time to fit residues: 408.2868 Evaluate side-chains 296 residues out of total 3300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 250 time to evaluate : 3.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 20 THR Chi-restraints excluded: chain E residue 94 PHE Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 495 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 580 GLN Chi-restraints excluded: chain A residue 729 VAL Chi-restraints excluded: chain A residue 825 LYS Chi-restraints excluded: chain A residue 878 LEU Chi-restraints excluded: chain A residue 1038 LYS Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 94 MET Chi-restraints excluded: chain F residue 47 LEU Chi-restraints excluded: chain C residue 198 TYR Chi-restraints excluded: chain C residue 309 GLU Chi-restraints excluded: chain C residue 317 ASN Chi-restraints excluded: chain C residue 613 GLN Chi-restraints excluded: chain C residue 1094 VAL Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 195 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain B residue 529 LYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 574 ASP Chi-restraints excluded: chain B residue 617 CYS Chi-restraints excluded: chain B residue 620 VAL Chi-restraints excluded: chain B residue 646 ARG Chi-restraints excluded: chain B residue 649 CYS Chi-restraints excluded: chain B residue 654 GLU Chi-restraints excluded: chain B residue 729 VAL Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 998 THR Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain I residue 69 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 235 optimal weight: 0.5980 chunk 315 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 272 optimal weight: 0.1980 chunk 43 optimal weight: 0.8980 chunk 82 optimal weight: 0.0270 chunk 296 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 304 optimal weight: 0.0670 chunk 37 optimal weight: 3.9990 chunk 54 optimal weight: 6.9990 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 779 GLN ** D 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 965 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.192549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.118674 restraints weight = 35737.683| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.74 r_work: 0.3131 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 30921 Z= 0.127 Angle : 0.492 9.275 42056 Z= 0.253 Chirality : 0.045 0.662 4811 Planarity : 0.004 0.049 5345 Dihedral : 5.093 59.562 4862 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.09 % Allowed : 13.82 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.51 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 0.34 (0.13), residues: 3715 helix: 1.75 (0.20), residues: 716 sheet: 0.52 (0.16), residues: 985 loop : -0.45 (0.13), residues: 2014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP F 96 HIS 0.002 0.001 HIS D 100 PHE 0.027 0.001 PHE C 166 TYR 0.038 0.001 TYR D 96 ARG 0.004 0.000 ARG F 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9631.19 seconds wall clock time: 176 minutes 20.70 seconds (10580.70 seconds total)