Starting phenix.real_space_refine on Wed Mar 20 01:39:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bon_16144/03_2024/8bon_16144_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bon_16144/03_2024/8bon_16144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bon_16144/03_2024/8bon_16144.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bon_16144/03_2024/8bon_16144.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bon_16144/03_2024/8bon_16144_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bon_16144/03_2024/8bon_16144_updated.pdb" } resolution = 3.2 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= 0.008 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 117 5.16 5 C 16509 2.51 5 N 4277 2.21 5 O 5027 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 25930 Number of models: 1 Model: "" Number of chains: 22 Chain: "B" Number of atoms: 8304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1070, 8304 Classifications: {'peptide': 1070} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 57, 'TRANS': 1012} Chain breaks: 4 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "E" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 158 Unusual residues: {'NH2': 1} Classifications: {'peptide': 18, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 1, 'TRANS': 16} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'CCS:plan-1': 1, 'CCS:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "D" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 158 Unusual residues: {'NH2': 1} Classifications: {'peptide': 18, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 1, 'TRANS': 16} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'CCS:plan-1': 1, 'CCS:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 8298 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1069, 8292 Classifications: {'peptide': 1069} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 1011} Chain breaks: 4 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 1069, 8292 Classifications: {'peptide': 1069} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 57, 'TRANS': 1011} Chain breaks: 4 Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 85 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 8483 Chain: "C" Number of atoms: 8168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8168 Classifications: {'peptide': 1053} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 56, 'TRANS': 996} Chain breaks: 7 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 39 Chain: "F" Number of atoms: 158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 158 Unusual residues: {'NH2': 1} Classifications: {'peptide': 18, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 1, 'TRANS': 16} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'CCS:plan-1': 1, 'CCS:plan-2': 1} Unresolved non-hydrogen planarities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "A" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 17.14, per 1000 atoms: 0.66 Number of scatterers: 25930 At special positions: 0 Unit cell: (152.323, 160.992, 196.906, 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 117 16.00 O 5027 8.00 N 4277 7.00 C 16509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=41, symmetry=0 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 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 738 " - pdb=" SG CYS B 760 " distance=2.02 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=2.02 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 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=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 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 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=6, symmetry=0 Links applied BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG A1302 " - " ASN A 343 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 709 " " NAG A1307 " - " ASN A 17 " " NAG A1308 " - " ASN A 282 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 709 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 17 " " NAG B1305 " - " ASN B 331 " " NAG B1306 " - " ASN B1074 " " NAG C1301 " - " ASN C 122 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 616 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C 234 " " NAG C1308 " - " ASN C 17 " " NAG C1309 " - " ASN C 331 " " NAG G 1 " - " ASN B 801 " " NAG H 1 " - " ASN B1098 " " NAG I 1 " - " ASN B1134 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 234 " " NAG L 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1134 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A 717 " " NAG P 1 " - " ASN C1098 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1134 " Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.22 Conformation dependent library (CDL) restraints added in 7.7 seconds 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6076 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 45 sheets defined 20.8% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.78 Creating SS restraints... Processing helix chain 'B' and resid 295 through 302 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.778A pdb=" N VAL B 341 " --> pdb=" O PHE B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 371 Processing helix chain 'B' and resid 407 through 409 No H-bonds generated for 'chain 'B' and resid 407 through 409' Processing helix chain 'B' and resid 417 through 421 Processing helix chain 'B' and resid 439 through 442 No H-bonds generated for 'chain 'B' and resid 439 through 442' Processing helix chain 'B' and resid 617 through 619 No H-bonds generated for 'chain 'B' and resid 617 through 619' Processing helix chain 'B' and resid 738 through 742 Processing helix chain 'B' and resid 747 through 756 removed outlier: 3.922A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 782 removed outlier: 3.623A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 825 Processing helix chain 'B' and resid 867 through 884 Processing helix chain 'B' and resid 898 through 909 Processing helix chain 'B' and resid 913 through 940 removed outlier: 5.883A pdb=" N LYS B 921 " --> pdb=" O TYR B 917 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU B 922 " --> pdb=" O GLU B 918 " (cutoff:3.500A) Processing helix chain 'B' and resid 946 through 967 removed outlier: 3.957A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU B 966 " --> pdb=" O LEU B 962 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N SER B 967 " --> pdb=" O VAL B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 977 through 983 Processing helix chain 'B' and resid 986 through 1032 removed outlier: 4.555A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 4.381A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 7 No H-bonds generated for 'chain 'D' and resid 5 through 7' Processing helix chain 'A' and resid 295 through 302 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.794A pdb=" N VAL A 341 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 387 through 389 No H-bonds generated for 'chain 'A' and resid 387 through 389' Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.512A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 439 through 442 No H-bonds generated for 'chain 'A' and resid 439 through 442' Processing helix chain 'A' and resid 617 through 619 No H-bonds generated for 'chain 'A' and resid 617 through 619' Processing helix chain 'A' and resid 738 through 741 No H-bonds generated for 'chain 'A' and resid 738 through 741' Processing helix chain 'A' and resid 747 through 756 removed outlier: 3.824A pdb=" N GLN A 755 " --> pdb=" O ASN A 751 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N TYR A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 782 removed outlier: 3.562A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 825 Processing helix chain 'A' and resid 867 through 884 Processing helix chain 'A' and resid 887 through 889 No H-bonds generated for 'chain 'A' and resid 887 through 889' Processing helix chain 'A' and resid 898 through 909 Processing helix chain 'A' and resid 913 through 917 Processing helix chain 'A' and resid 920 through 940 removed outlier: 3.744A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 944 through 967 removed outlier: 4.193A pdb=" N LYS A 947 " --> pdb=" O ALA A 944 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 949 " --> pdb=" O GLY A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 983 Processing helix chain 'A' and resid 986 through 1032 removed outlier: 5.423A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.874A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 303 Processing helix chain 'C' and resid 338 through 341 No H-bonds generated for 'chain 'C' and resid 338 through 341' Processing helix chain 'C' and resid 365 through 369 Processing helix chain 'C' and resid 407 through 409 No H-bonds generated for 'chain 'C' and resid 407 through 409' Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'C' and resid 738 through 741 No H-bonds generated for 'chain 'C' and resid 738 through 741' Processing helix chain 'C' and resid 747 through 756 removed outlier: 3.554A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N TYR C 756 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 782 removed outlier: 3.534A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 817 through 824 removed outlier: 3.530A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 867 through 883 Processing helix chain 'C' and resid 887 through 889 No H-bonds generated for 'chain 'C' and resid 887 through 889' Processing helix chain 'C' and resid 898 through 909 Processing helix chain 'C' and resid 913 through 940 removed outlier: 5.892A pdb=" N LYS C 921 " --> pdb=" O TYR C 917 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N LEU C 922 " --> pdb=" O GLU C 918 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 942 through 967 removed outlier: 4.599A pdb=" N LYS C 947 " --> pdb=" O ALA C 944 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN C 949 " --> pdb=" O GLY C 946 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASP C 950 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL C 951 " --> pdb=" O LEU C 948 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN C 954 " --> pdb=" O VAL C 951 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN C 955 " --> pdb=" O VAL C 952 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN C 960 " --> pdb=" O GLN C 957 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR C 961 " --> pdb=" O ALA C 958 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 963 " --> pdb=" O ASN C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 977 through 981 Processing helix chain 'C' and resid 986 through 1032 removed outlier: 3.549A pdb=" N GLU C 990 " --> pdb=" O PRO C 986 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU C 996 " --> pdb=" O GLN C 992 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 removed outlier: 4.370A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.801A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ALA B 264 " --> pdb=" O THR B 95 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR B 95 " --> pdb=" O ALA B 264 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.617A pdb=" N VAL B 289 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 166 through 171 removed outlier: 7.305A pdb=" N VAL B 130 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLU B 169 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE B 128 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL B 171 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N VAL B 126 " --> pdb=" O VAL B 171 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N LEU B 241 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N TRP B 104 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLN B 239 " --> pdb=" O TRP B 104 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N PHE B 106 " --> pdb=" O ARG B 237 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ARG B 237 " --> pdb=" O PHE B 106 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 156 through 158 removed outlier: 3.893A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE B 140 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 325 through 327 removed outlier: 8.720A pdb=" N ILE B 326 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ASN B 540 " --> pdb=" O ILE B 326 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.305A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 361 through 363 removed outlier: 3.780A pdb=" N CYS B 525 " --> pdb=" O CYS B 361 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 452 through 454 Processing sheet with id= I, first strand: chain 'B' and resid 642 through 645 removed outlier: 4.444A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 691 through 696 removed outlier: 6.196A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 711 through 715 Processing sheet with id= L, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.042A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.358A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 1088 through 1090 Processing sheet with id= O, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id= P, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.566A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA A 264 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR A 95 " --> pdb=" O ALA A 264 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 227 " --> pdb=" O ILE A 203 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.880A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'A' and resid 83 through 85 Processing sheet with id= S, first strand: chain 'A' and resid 116 through 121 removed outlier: 3.568A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'A' and resid 243 through 246 removed outlier: 6.936A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N ARG A 246 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N VAL A 143 " --> pdb=" O ARG A 246 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N TYR A 144 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU A 154 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.811A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'A' and resid 452 through 454 Processing sheet with id= W, first strand: chain 'A' and resid 538 through 543 removed outlier: 3.918A pdb=" N PHE A 543 " --> pdb=" O LEU A 546 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP A 574 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'A' and resid 642 through 645 removed outlier: 4.272A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'A' and resid 691 through 696 removed outlier: 6.447A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'A' and resid 711 through 715 Processing sheet with id= AA, first strand: chain 'A' and resid 718 through 728 removed outlier: 5.845A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.238A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'A' and resid 1088 through 1090 Processing sheet with id= AD, first strand: chain 'A' and resid 1094 through 1097 Processing sheet with id= AE, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.955A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.883A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'C' and resid 116 through 121 removed outlier: 3.852A pdb=" N VAL C 130 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'C' and resid 243 through 246 removed outlier: 7.197A pdb=" N LEU C 141 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ARG C 246 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N VAL C 143 " --> pdb=" O ARG C 246 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE C 140 " --> pdb=" O ARG C 158 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG C 158 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N TYR C 144 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N GLU C 154 " --> pdb=" O TYR C 144 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N HIS C 146 " --> pdb=" O TRP C 152 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N TRP C 152 " --> pdb=" O HIS C 146 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'C' and resid 324 through 327 Processing sheet with id= AJ, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.472A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.559A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'C' and resid 551 through 554 Processing sheet with id= AM, first strand: chain 'C' and resid 642 through 645 removed outlier: 3.612A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'C' and resid 691 through 696 removed outlier: 5.937A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.708A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'C' and resid 718 through 728 removed outlier: 5.929A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.363A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'C' and resid 1088 through 1090 Processing sheet with id= AS, first strand: chain 'C' and resid 101 through 107 removed outlier: 6.967A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) 858 hydrogen bonds defined for protein. 2333 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: 10.22 Time building geometry restraints manager: 10.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4176 1.32 - 1.44: 7518 1.44 - 1.57: 14685 1.57 - 1.69: 1 1.69 - 1.82: 151 Bond restraints: 26531 Sorted by residual: bond pdb=" CG PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 1.503 1.191 0.312 3.40e-02 8.65e+02 8.40e+01 bond pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 1.473 1.567 -0.094 1.40e-02 5.10e+03 4.49e+01 bond pdb=" N PRO A 384 " pdb=" CA PRO A 384 " ideal model delta sigma weight residual 1.469 1.410 0.059 1.28e-02 6.10e+03 2.10e+01 bond pdb=" CB PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 1.492 1.709 -0.217 5.00e-02 4.00e+02 1.88e+01 bond pdb=" CD CCS D 17 " pdb=" CE CCS D 17 " ideal model delta sigma weight residual 1.548 1.499 0.049 2.00e-02 2.50e+03 6.09e+00 ... (remaining 26526 not shown) Histogram of bond angle deviations from ideal: 87.19 - 97.42: 7 97.42 - 107.66: 1029 107.66 - 117.89: 19025 117.89 - 128.13: 15941 128.13 - 138.36: 142 Bond angle restraints: 36144 Sorted by residual: angle pdb=" CA PRO A 384 " pdb=" N PRO A 384 " pdb=" CD PRO A 384 " ideal model delta sigma weight residual 112.00 92.68 19.32 1.40e+00 5.10e-01 1.90e+02 angle pdb=" N PRO A 384 " pdb=" CD PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 103.20 87.19 16.01 1.50e+00 4.44e-01 1.14e+02 angle pdb=" SG CCS E 17 " pdb=" CD CCS E 17 " pdb=" CE CCS E 17 " ideal model delta sigma weight residual 117.40 138.36 -20.96 3.00e+00 1.11e-01 4.88e+01 angle pdb=" SG CCS F 17 " pdb=" CD CCS F 17 " pdb=" CE CCS F 17 " ideal model delta sigma weight residual 117.40 137.93 -20.53 3.00e+00 1.11e-01 4.68e+01 angle pdb=" CA PRO A 384 " pdb=" CB PRO A 384 " pdb=" CG PRO A 384 " ideal model delta sigma weight residual 104.50 92.74 11.76 1.90e+00 2.77e-01 3.83e+01 ... (remaining 36139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 14997 17.95 - 35.89: 1112 35.89 - 53.84: 216 53.84 - 71.79: 60 71.79 - 89.73: 22 Dihedral angle restraints: 16407 sinusoidal: 6961 harmonic: 9446 Sorted by residual: dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.64 72.64 1 1.00e+01 1.00e-02 6.74e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -144.78 58.78 1 1.00e+01 1.00e-02 4.62e+01 dihedral pdb=" CB CYS C 617 " pdb=" SG CYS C 617 " pdb=" SG CYS C 649 " pdb=" CB CYS C 649 " ideal model delta sinusoidal sigma weight residual 93.00 142.03 -49.03 1 1.00e+01 1.00e-02 3.31e+01 ... (remaining 16404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 3615 0.063 - 0.126: 604 0.126 - 0.189: 13 0.189 - 0.252: 4 0.252 - 0.315: 2 Chirality restraints: 4238 Sorted by residual: chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" C1 NAG A1304 " pdb=" ND2 ASN A 616 " pdb=" C2 NAG A1304 " pdb=" O5 NAG A1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" C1 NAG B1306 " pdb=" ND2 ASN B1074 " pdb=" C2 NAG B1306 " pdb=" O5 NAG B1306 " both_signs ideal model delta sigma weight residual False -2.40 -2.17 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 4235 not shown) Planarity restraints: 4658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " 0.112 5.00e-02 4.00e+02 1.50e-01 3.61e+01 pdb=" N PRO A 384 " -0.259 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " 0.075 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 208 " 0.065 5.00e-02 4.00e+02 9.40e-02 1.41e+01 pdb=" N PRO B 209 " -0.162 5.00e-02 4.00e+02 pdb=" CA PRO B 209 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 209 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 233 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.55e+00 pdb=" C ILE A 233 " -0.048 2.00e-02 2.50e+03 pdb=" O ILE A 233 " 0.018 2.00e-02 2.50e+03 pdb=" N ASN A 234 " 0.016 2.00e-02 2.50e+03 ... (remaining 4655 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 645 2.70 - 3.25: 24706 3.25 - 3.80: 39986 3.80 - 4.35: 53224 4.35 - 4.90: 90312 Nonbonded interactions: 208873 Sorted by model distance: nonbonded pdb=" O ILE A 233 " pdb=" N2 NAG A1303 " model vdw 2.145 2.520 nonbonded pdb=" OH TYR B 91 " pdb=" OE1 GLU B 191 " model vdw 2.208 2.440 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.210 2.440 nonbonded pdb=" OE2 GLU C 298 " pdb=" OG SER C 316 " model vdw 2.214 2.440 nonbonded pdb=" OG1 THR A 108 " pdb=" O ASN A 234 " model vdw 2.216 2.440 ... (remaining 208868 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 14 through 69 or resid 76 through 183 or resid 188 through \ 209 or resid 219 through 247 or resid 251 through 308 or (resid 309 and (name N \ or name CA or name C or name O or name CB )) or resid 310 through 492 or resid \ 494 through 528 or (resid 529 and (name N or name CA or name C or name O or name \ CB )) or resid 530 through 553 or (resid 554 and (name N or name CA or name C o \ r name O or name CB )) or resid 555 through 793 or (resid 794 and (name N or nam \ e CA or name C or name O or name CB )) or resid 795 or (resid 796 and (name N or \ name CA or name C or name O or name CB )) or resid 797 through 1141 or (resid 1 \ 142 and (name N or name CA or name C or name O or name CB )) or resid 1143 throu \ gh 1144 or (resid 1145 through 1146 and (name N or name CA or name C or name O o \ r name CB )) or resid 1147 or resid 1301 through 1306)) selection = (chain 'B' and (resid 14 through 69 or resid 76 through 183 or resid 188 through \ 209 or resid 219 through 247 or resid 251 through 492 or resid 494 through 581 \ or (resid 582 through 583 and (name N or name CA or name C or name O or name CB \ )) or resid 584 through 585 or (resid 586 and (name N or name CA or name C or na \ me O or name CB )) or resid 587 through 613 or (resid 614 and (name N or name CA \ or name C or name O or name CB )) or resid 615 through 618 or (resid 619 and (n \ ame N or name CA or name C or name O or name CB )) or resid 620 through 676 or r \ esid 690 through 744 or (resid 745 and (name N or name CA or name C or name O or \ name CB )) or resid 746 through 920 or (resid 921 and (name N or name CA or nam \ e C or name O or name CB )) or resid 922 through 1072 or (resid 1073 and (name N \ or name CA or name C or name O or name CB )) or resid 1074 through 1117 or (res \ id 1118 and (name N or name CA or name C or name O or name CB )) or resid 1119 t \ hrough 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name \ O or name CB )) or resid 1147 or resid 1301 through 1306)) selection = (chain 'C' and (resid 14 through 457 or (resid 458 and (name N or name CA or nam \ e C or name O or name CB )) or resid 459 through 492 or resid 494 through 581 or \ (resid 582 through 583 and (name N or name CA or name C or name O or name CB )) \ or resid 584 through 585 or (resid 586 and (name N or name CA or name C or name \ O or name CB )) or resid 587 through 613 or (resid 614 and (name N or name CA o \ r name C or name O or name CB )) or resid 615 through 618 or (resid 619 and (nam \ e N or name CA or name C or name O or name CB )) or resid 620 through 676 or res \ id 690 through 744 or (resid 745 and (name N or name CA or name C or name O or n \ ame CB )) or resid 746 through 920 or (resid 921 and (name N or name CA or name \ C or name O or name CB )) or resid 922 through 1072 or (resid 1073 and (name N o \ r name CA or name C or name O or name CB )) or resid 1074 through 1117 or (resid \ 1118 and (name N or name CA or name C or name O or name CB )) or resid 1119 thr \ ough 1143 or (resid 1144 through 1146 and (name N or name CA or name C or name O \ or name CB )) or resid 1147 or resid 1301 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.620 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: 6.840 Check model and map are aligned: 0.340 Set scattering table: 0.210 Process input model: 71.910 Find NCS groups from input model: 2.190 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 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 0.312 26531 Z= 0.285 Angle : 0.568 20.964 36144 Z= 0.281 Chirality : 0.044 0.315 4238 Planarity : 0.004 0.150 4624 Dihedral : 13.294 89.735 10208 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.15), residues: 3199 helix: 1.35 (0.21), residues: 648 sheet: 0.60 (0.20), residues: 724 loop : -0.56 (0.14), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 886 HIS 0.003 0.001 HIS C1083 PHE 0.026 0.001 PHE A 168 TYR 0.013 0.001 TYR B1067 ARG 0.004 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 2.467 Fit side-chains REVERT: A 168 PHE cc_start: 0.6763 (t80) cc_final: 0.6542 (t80) REVERT: A 384 PRO cc_start: 0.6775 (Cg_exo) cc_final: 0.6361 (Cg_exo) REVERT: C 238 PHE cc_start: 0.7312 (p90) cc_final: 0.7051 (p90) REVERT: C 950 ASP cc_start: 0.7788 (m-30) cc_final: 0.7442 (m-30) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.3453 time to fit residues: 120.8743 Evaluate side-chains 167 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 271 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 83 optimal weight: 0.0770 chunk 164 optimal weight: 7.9990 chunk 129 optimal weight: 0.6980 chunk 251 optimal weight: 50.0000 chunk 97 optimal weight: 0.5980 chunk 152 optimal weight: 10.0000 chunk 187 optimal weight: 0.0050 chunk 291 optimal weight: 0.4980 overall best weight: 0.3752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN A 218 GLN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.0636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 26531 Z= 0.154 Angle : 0.494 9.254 36144 Z= 0.255 Chirality : 0.044 0.335 4238 Planarity : 0.004 0.070 4624 Dihedral : 6.634 58.393 4518 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 0.39 % Allowed : 4.15 % Favored : 95.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3199 helix: 1.79 (0.21), residues: 651 sheet: 0.61 (0.20), residues: 706 loop : -0.53 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 886 HIS 0.003 0.000 HIS C 207 PHE 0.025 0.001 PHE C 168 TYR 0.017 0.001 TYR B1067 ARG 0.003 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 183 time to evaluate : 2.796 Fit side-chains revert: symmetry clash REVERT: C 950 ASP cc_start: 0.7455 (m-30) cc_final: 0.7104 (m-30) outliers start: 11 outliers final: 9 residues processed: 193 average time/residue: 0.3327 time to fit residues: 107.3058 Evaluate side-chains 172 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 163 time to evaluate : 2.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 386 LYS Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 588 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 162 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 242 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 292 optimal weight: 0.9980 chunk 315 optimal weight: 0.5980 chunk 260 optimal weight: 40.0000 chunk 289 optimal weight: 0.0870 chunk 99 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 overall best weight: 0.8560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN ** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 935 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26531 Z= 0.205 Angle : 0.495 9.861 36144 Z= 0.253 Chirality : 0.045 0.328 4238 Planarity : 0.003 0.034 4624 Dihedral : 5.877 58.149 4518 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.79 % Allowed : 6.05 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.15), residues: 3199 helix: 1.72 (0.21), residues: 656 sheet: 0.52 (0.19), residues: 724 loop : -0.52 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 886 HIS 0.004 0.001 HIS C1083 PHE 0.030 0.001 PHE A 238 TYR 0.020 0.001 TYR B1067 ARG 0.002 0.000 ARG C 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 177 time to evaluate : 2.754 Fit side-chains REVERT: B 140 PHE cc_start: 0.7789 (p90) cc_final: 0.7551 (p90) REVERT: C 950 ASP cc_start: 0.7491 (m-30) cc_final: 0.7147 (m-30) outliers start: 22 outliers final: 17 residues processed: 192 average time/residue: 0.3541 time to fit residues: 112.2432 Evaluate side-chains 186 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 169 time to evaluate : 2.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 998 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 288 optimal weight: 0.9980 chunk 219 optimal weight: 3.9990 chunk 151 optimal weight: 0.0060 chunk 32 optimal weight: 30.0000 chunk 139 optimal weight: 4.9990 chunk 196 optimal weight: 0.9980 chunk 293 optimal weight: 2.9990 chunk 310 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 277 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 1.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 926 GLN C 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26531 Z= 0.224 Angle : 0.500 10.053 36144 Z= 0.254 Chirality : 0.045 0.350 4238 Planarity : 0.003 0.034 4624 Dihedral : 5.490 56.656 4518 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.00 % Allowed : 6.94 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.15), residues: 3199 helix: 1.65 (0.21), residues: 657 sheet: 0.53 (0.19), residues: 736 loop : -0.54 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 886 HIS 0.004 0.001 HIS C1083 PHE 0.023 0.001 PHE A 168 TYR 0.019 0.001 TYR B1067 ARG 0.005 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 174 time to evaluate : 2.776 Fit side-chains REVERT: C 950 ASP cc_start: 0.7603 (m-30) cc_final: 0.7254 (m-30) outliers start: 28 outliers final: 26 residues processed: 194 average time/residue: 0.3326 time to fit residues: 107.1789 Evaluate side-chains 191 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 165 time to evaluate : 2.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 492 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 258 optimal weight: 8.9990 chunk 176 optimal weight: 2.9990 chunk 4 optimal weight: 0.0770 chunk 231 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 264 optimal weight: 4.9990 chunk 214 optimal weight: 0.8980 chunk 0 optimal weight: 20.0000 chunk 158 optimal weight: 5.9990 chunk 278 optimal weight: 4.9990 chunk 78 optimal weight: 0.0980 overall best weight: 1.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 784 GLN B 926 GLN C 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 26531 Z= 0.369 Angle : 0.565 9.698 36144 Z= 0.288 Chirality : 0.047 0.344 4238 Planarity : 0.004 0.036 4624 Dihedral : 5.497 56.964 4518 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.22 % Allowed : 7.95 % Favored : 90.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.15), residues: 3199 helix: 1.32 (0.21), residues: 656 sheet: 0.40 (0.19), residues: 743 loop : -0.63 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 886 HIS 0.006 0.001 HIS C1083 PHE 0.023 0.002 PHE A 168 TYR 0.021 0.001 TYR B1067 ARG 0.007 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 170 time to evaluate : 2.969 Fit side-chains REVERT: B 784 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8042 (mt0) outliers start: 34 outliers final: 29 residues processed: 193 average time/residue: 0.3242 time to fit residues: 105.9974 Evaluate side-chains 191 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 2.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 549 THR Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 784 GLN Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 994 ASP Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 104 optimal weight: 0.9980 chunk 279 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 182 optimal weight: 0.5980 chunk 76 optimal weight: 0.3980 chunk 310 optimal weight: 0.6980 chunk 257 optimal weight: 50.0000 chunk 143 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 87 ASN A 388 ASN C 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 26531 Z= 0.182 Angle : 0.496 10.014 36144 Z= 0.252 Chirality : 0.044 0.361 4238 Planarity : 0.003 0.045 4624 Dihedral : 5.126 56.525 4518 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 0.89 % Allowed : 8.88 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.15), residues: 3199 helix: 1.59 (0.21), residues: 658 sheet: 0.42 (0.19), residues: 737 loop : -0.58 (0.14), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 886 HIS 0.003 0.001 HIS C1083 PHE 0.025 0.001 PHE A 92 TYR 0.018 0.001 TYR B 266 ARG 0.003 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 165 time to evaluate : 2.733 Fit side-chains REVERT: C 129 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7319 (tptt) REVERT: C 950 ASP cc_start: 0.7555 (m-30) cc_final: 0.7212 (m-30) outliers start: 25 outliers final: 22 residues processed: 183 average time/residue: 0.3350 time to fit residues: 102.5870 Evaluate side-chains 183 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 160 time to evaluate : 2.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 299 optimal weight: 0.8980 chunk 35 optimal weight: 30.0000 chunk 176 optimal weight: 2.9990 chunk 226 optimal weight: 9.9990 chunk 175 optimal weight: 0.9980 chunk 261 optimal weight: 50.0000 chunk 173 optimal weight: 2.9990 chunk 309 optimal weight: 0.0040 chunk 193 optimal weight: 0.9990 chunk 188 optimal weight: 0.5980 chunk 142 optimal weight: 7.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26531 Z= 0.181 Angle : 0.489 10.078 36144 Z= 0.248 Chirality : 0.044 0.363 4238 Planarity : 0.003 0.043 4624 Dihedral : 4.871 56.465 4518 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.18 % Allowed : 8.91 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.15), residues: 3199 helix: 1.70 (0.21), residues: 657 sheet: 0.45 (0.19), residues: 735 loop : -0.55 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 886 HIS 0.003 0.001 HIS C1083 PHE 0.025 0.001 PHE A 92 TYR 0.017 0.001 TYR B1067 ARG 0.006 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 167 time to evaluate : 3.082 Fit side-chains REVERT: A 241 LEU cc_start: 0.6441 (OUTLIER) cc_final: 0.5967 (pp) REVERT: C 129 LYS cc_start: 0.7583 (OUTLIER) cc_final: 0.7291 (tptp) REVERT: C 950 ASP cc_start: 0.7511 (m-30) cc_final: 0.7155 (m-30) outliers start: 33 outliers final: 26 residues processed: 189 average time/residue: 0.3440 time to fit residues: 108.8347 Evaluate side-chains 190 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 162 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 551 VAL Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 191 optimal weight: 1.9990 chunk 123 optimal weight: 0.0670 chunk 184 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 196 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 152 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 243 optimal weight: 4.9990 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN A 207 HIS A 388 ASN C 66 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26531 Z= 0.224 Angle : 0.503 10.035 36144 Z= 0.255 Chirality : 0.045 0.361 4238 Planarity : 0.003 0.045 4624 Dihedral : 4.818 56.593 4518 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.11 % Allowed : 9.38 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 3199 helix: 1.62 (0.21), residues: 658 sheet: 0.42 (0.19), residues: 736 loop : -0.57 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 886 HIS 0.003 0.001 HIS C1083 PHE 0.024 0.001 PHE A 168 TYR 0.019 0.001 TYR B1067 ARG 0.005 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 2.784 Fit side-chains REVERT: A 241 LEU cc_start: 0.6480 (OUTLIER) cc_final: 0.5997 (pp) REVERT: A 988 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6888 (tm-30) REVERT: C 129 LYS cc_start: 0.7555 (OUTLIER) cc_final: 0.7140 (tptp) REVERT: C 950 ASP cc_start: 0.7584 (m-30) cc_final: 0.7219 (m-30) outliers start: 31 outliers final: 27 residues processed: 183 average time/residue: 0.3367 time to fit residues: 103.5313 Evaluate side-chains 190 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 161 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 281 optimal weight: 0.9980 chunk 296 optimal weight: 1.9990 chunk 270 optimal weight: 4.9990 chunk 288 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 125 optimal weight: 20.0000 chunk 226 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 260 optimal weight: 50.0000 chunk 272 optimal weight: 2.9990 chunk 287 optimal weight: 0.7980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN A 207 HIS C 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 26531 Z= 0.348 Angle : 0.552 9.845 36144 Z= 0.280 Chirality : 0.047 0.356 4238 Planarity : 0.004 0.043 4624 Dihedral : 4.993 56.888 4518 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.18 % Allowed : 9.41 % Favored : 89.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3199 helix: 1.38 (0.21), residues: 658 sheet: 0.32 (0.19), residues: 746 loop : -0.63 (0.14), residues: 1795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 886 HIS 0.005 0.001 HIS B1064 PHE 0.023 0.002 PHE A 168 TYR 0.023 0.001 TYR B1067 ARG 0.006 0.000 ARG A1039 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 166 time to evaluate : 3.099 Fit side-chains REVERT: A 241 LEU cc_start: 0.6576 (OUTLIER) cc_final: 0.6076 (pp) REVERT: A 988 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6980 (tm-30) REVERT: C 129 LYS cc_start: 0.7595 (OUTLIER) cc_final: 0.7157 (tptp) REVERT: C 950 ASP cc_start: 0.7619 (m-30) cc_final: 0.7301 (m-30) REVERT: C 984 LEU cc_start: 0.8410 (mp) cc_final: 0.8203 (mp) outliers start: 33 outliers final: 29 residues processed: 187 average time/residue: 0.3310 time to fit residues: 103.7340 Evaluate side-chains 192 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 161 time to evaluate : 2.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 PHE Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 901 GLN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 936 ASP Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 998 THR Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 189 optimal weight: 0.5980 chunk 304 optimal weight: 1.9990 chunk 186 optimal weight: 0.0980 chunk 144 optimal weight: 0.9990 chunk 211 optimal weight: 0.4980 chunk 319 optimal weight: 2.9990 chunk 294 optimal weight: 0.6980 chunk 254 optimal weight: 50.0000 chunk 26 optimal weight: 4.9990 chunk 196 optimal weight: 0.8980 chunk 156 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS C 66 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 26531 Z= 0.165 Angle : 0.495 10.102 36144 Z= 0.249 Chirality : 0.044 0.367 4238 Planarity : 0.003 0.049 4624 Dihedral : 4.715 56.347 4518 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.97 % Allowed : 9.77 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 3199 helix: 1.68 (0.21), residues: 656 sheet: 0.38 (0.19), residues: 738 loop : -0.57 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 886 HIS 0.003 0.001 HIS C1083 PHE 0.026 0.001 PHE A 92 TYR 0.016 0.001 TYR A1067 ARG 0.007 0.000 ARG C 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6398 Ramachandran restraints generated. 3199 Oldfield, 0 Emsley, 3199 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 2.916 Fit side-chains REVERT: A 241 LEU cc_start: 0.6614 (OUTLIER) cc_final: 0.6151 (pp) REVERT: A 988 GLU cc_start: 0.7178 (tm-30) cc_final: 0.6910 (tm-30) REVERT: C 129 LYS cc_start: 0.7557 (OUTLIER) cc_final: 0.7099 (tptp) REVERT: C 950 ASP cc_start: 0.7571 (m-30) cc_final: 0.7196 (m-30) outliers start: 27 outliers final: 24 residues processed: 178 average time/residue: 0.3321 time to fit residues: 99.4279 Evaluate side-chains 184 residues out of total 2844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 158 time to evaluate : 2.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 126 VAL Chi-restraints excluded: chain B residue 130 VAL Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 586 ASP Chi-restraints excluded: chain B residue 725 GLU Chi-restraints excluded: chain B residue 856 ASN Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 241 LEU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 441 LEU Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 976 VAL Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 588 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 650 LEU Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 977 LEU Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 202 optimal weight: 0.8980 chunk 271 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 234 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 255 optimal weight: 50.0000 chunk 106 optimal weight: 2.9990 chunk 261 optimal weight: 0.0060 chunk 32 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 901 GLN A 207 HIS C 66 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.194903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.164547 restraints weight = 44154.897| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.14 r_work: 0.3626 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3579 r_free = 0.3579 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26531 Z= 0.211 Angle : 0.502 10.082 36144 Z= 0.253 Chirality : 0.044 0.364 4238 Planarity : 0.003 0.045 4624 Dihedral : 4.673 56.565 4518 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.97 % Allowed : 9.84 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.15), residues: 3199 helix: 1.67 (0.21), residues: 658 sheet: 0.38 (0.19), residues: 739 loop : -0.57 (0.14), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 886 HIS 0.003 0.001 HIS C1083 PHE 0.025 0.001 PHE A 92 TYR 0.018 0.001 TYR B1067 ARG 0.007 0.000 ARG C 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4678.18 seconds wall clock time: 86 minutes 15.33 seconds (5175.33 seconds total)