Starting phenix.real_space_refine on Fri Jul 26 17:57:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc3_39921/07_2024/8zc3_39921.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc3_39921/07_2024/8zc3_39921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc3_39921/07_2024/8zc3_39921.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc3_39921/07_2024/8zc3_39921.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc3_39921/07_2024/8zc3_39921.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zc3_39921/07_2024/8zc3_39921.cif" } resolution = 4.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.037 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 144 5.16 5 C 21556 2.51 5 N 5557 2.21 5 O 6599 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 562": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A TYR 873": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 888": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 979": "OD1" <-> "OD2" Residue "B ASP 53": "OD1" <-> "OD2" Residue "B GLU 406": "OE1" <-> "OE2" Residue "B PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 340": "OE1" <-> "OE2" Residue "C TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 802": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 820": "OD1" <-> "OD2" Residue "C PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "E TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 84": "OE1" <-> "OE2" Residue "M TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 171": "OE1" <-> "OE2" Residue "Q PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 54": "OD1" <-> "OD2" Residue "R TYR 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 33856 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 7778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7778 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 55, 'TRANS': 937} Chain breaks: 10 Chain: "B" Number of atoms: 7790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 994, 7790 Classifications: {'peptide': 994} Link IDs: {'PTRANS': 55, 'TRANS': 938} Chain breaks: 10 Chain: "C" Number of atoms: 7778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 7778 Classifications: {'peptide': 993} Link IDs: {'PTRANS': 55, 'TRANS': 937} Chain breaks: 10 Chain: "D" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "E" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Chain: "M" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "N" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1591 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 195} Chain breaks: 1 Chain: "Q" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Chain: "R" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1679 Classifications: {'peptide': 221} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 208} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "B" 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 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: 16.76, per 1000 atoms: 0.50 Number of scatterers: 33856 At special positions: 0 Unit cell: (136.576, 199.936, 242.176, 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 144 16.00 O 6599 8.00 N 5557 7.00 C 21556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=51, symmetry=0 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS 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 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D 145 " - pdb=" SG CYS D 204 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 103 " - pdb=" SG CYS E 108 " distance=2.03 Simple disulfide: pdb=" SG CYS E 154 " - pdb=" SG CYS E 210 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 145 " - pdb=" SG CYS M 204 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 89 " distance=2.03 Simple disulfide: pdb=" SG CYS N 145 " - pdb=" SG CYS N 204 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 103 " - pdb=" SG CYS Q 108 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 154 " - pdb=" SG CYS Q 210 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 103 " - pdb=" SG CYS R 108 " distance=2.03 Simple disulfide: pdb=" SG CYS R 154 " - pdb=" SG CYS R 210 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " 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 O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 603 " " NAG A1304 " - " ASN A 616 " " NAG A1305 " - " ASN A 657 " " NAG A1306 " - " ASN A 709 " " NAG A1307 " - " ASN A1074 " " NAG A1308 " - " ASN A1134 " " NAG A1309 " - " ASN A 61 " " NAG A1310 " - " ASN A 234 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 234 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B1098 " " NAG B1308 " - " ASN B1134 " " NAG B1309 " - " ASN B 343 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 234 " " NAG C1305 " - " ASN C 616 " " NAG C1306 " - " ASN C 657 " " NAG C1307 " - " ASN C 709 " " NAG C1308 " - " ASN C1074 " " NAG C1309 " - " ASN C 343 " " NAG F 1 " - " ASN A 717 " " NAG G 1 " - " ASN A 801 " " NAG H 1 " - " ASN A1098 " " NAG I 1 " - " ASN B 122 " " NAG J 1 " - " ASN B 717 " " NAG K 1 " - " ASN B 801 " " NAG L 1 " - " ASN B 331 " " NAG O 1 " - " ASN C 717 " " NAG P 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1098 " " NAG T 1 " - " ASN C1134 " Time building additional restraints: 12.59 Conformation dependent library (CDL) restraints added in 5.7 seconds 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8000 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 70 sheets defined 16.7% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.36 Creating SS restraints... Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.864A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.542A pdb=" N PHE A 371 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 removed outlier: 3.616A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 4.263A pdb=" N SER A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.992A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 916 removed outlier: 3.592A pdb=" N LEU A 916 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.968A pdb=" N SER A 939 " --> pdb=" O GLN A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 966 removed outlier: 3.701A pdb=" N LEU A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 984 removed outlier: 3.592A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N SER A 982 " --> pdb=" O ASN A 978 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG A 983 " --> pdb=" O ASP A 979 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 977 through 984' Processing helix chain 'A' and resid 985 through 1032 removed outlier: 4.394A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 369 Processing helix chain 'B' and resid 383 through 387 removed outlier: 3.685A pdb=" N LYS B 386 " --> pdb=" O SER B 383 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 383 through 387' Processing helix chain 'B' and resid 405 through 407 No H-bonds generated for 'chain 'B' and resid 405 through 407' Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.832A pdb=" N SER B 750 " --> pdb=" O SER B 746 " (cutoff:3.500A) Processing helix chain 'B' and resid 760 through 781 Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.676A pdb=" N ILE B 870 " --> pdb=" O THR B 866 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 910 Processing helix chain 'B' and resid 913 through 919 removed outlier: 4.317A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU B 918 " --> pdb=" O ASN B 914 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN B 919 " --> pdb=" O VAL B 915 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 913 through 919' Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.846A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 3.972A pdb=" N GLU B 990 " --> pdb=" O PRO B 986 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.813A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP B1146 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.531A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N TYR C 369 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 365 through 370' Processing helix chain 'C' and resid 502 through 506 removed outlier: 3.613A pdb=" N GLN C 506 " --> pdb=" O VAL C 503 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 removed outlier: 3.529A pdb=" N TYR C 741 " --> pdb=" O ASP C 737 " (cutoff:3.500A) Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.505A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU C 754 " --> pdb=" O SER C 750 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.500A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU C 763 " --> pdb=" O PHE C 759 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE C 782 " --> pdb=" O THR C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 913 through 919 removed outlier: 3.739A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ASN C 919 " --> pdb=" O VAL C 915 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 967 removed outlier: 3.692A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N SER C 967 " --> pdb=" O VAL C 963 " (cutoff:3.500A) Processing helix chain 'C' and resid 979 through 984 Processing helix chain 'C' and resid 991 through 1033 removed outlier: 3.581A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 138 removed outlier: 3.865A pdb=" N LEU D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 199 removed outlier: 3.749A pdb=" N HIS D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 111 removed outlier: 3.715A pdb=" N ARG E 110 " --> pdb=" O SER E 107 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 139 removed outlier: 3.513A pdb=" N ASN M 139 " --> pdb=" O LEU M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 192 through 199 removed outlier: 3.591A pdb=" N HIS M 199 " --> pdb=" O GLN M 195 " (cutoff:3.500A) Processing helix chain 'N' and resid 132 through 137 Processing helix chain 'N' and resid 192 through 199 Processing helix chain 'Q' and resid 87 through 91 removed outlier: 3.902A pdb=" N THR Q 91 " --> pdb=" O SER Q 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 170 through 172 No H-bonds generated for 'chain 'R' and resid 170 through 172' Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.705A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 191 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 4.257A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY B 548 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY B 550 " --> pdb=" O VAL B 539 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL B 539 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE B 326 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 49 through 55 removed outlier: 3.651A pdb=" N HIS A 49 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 55 " --> pdb=" O GLN A 271 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN A 271 " --> pdb=" O PHE A 55 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU A 276 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.739A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A 107 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE A 119 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 126 " --> pdb=" O SER A 172 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 140 through 141 removed outlier: 4.461A pdb=" N PHE A 140 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG A 158 " --> pdb=" O PHE A 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 6.651A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER A 316 " --> pdb=" O VAL A 595 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 598 " --> pdb=" O ALA A 609 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N CYS A 649 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 650 " --> pdb=" O PHE A 643 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE A 643 " --> pdb=" O LEU A 650 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 3.583A pdb=" N THR A 588 " --> pdb=" O VAL A 551 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.613A pdb=" N LYS A 356 " --> pdb=" O ALA A 397 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.759A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.887A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 9.446A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 721 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 712 through 721 current: chain 'A' and resid 1059 through 1077 removed outlier: 3.520A pdb=" N THR A1105 " --> pdb=" O VAL A1094 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.032A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 788 through 789 removed outlier: 6.101A pdb=" N ILE A 788 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 5.041A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.663A pdb=" N VAL B 62 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER B 31 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR B 265 " --> pdb=" O PHE B 65 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 49 through 55 removed outlier: 3.501A pdb=" N LEU B 277 " --> pdb=" O HIS B 49 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N THR B 51 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE B 275 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS B 278 " --> pdb=" O ASP B 287 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.517A pdb=" N PHE B 238 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU B 241 " --> pdb=" O GLY B 103 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 119 through 121 removed outlier: 4.252A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'B' and resid 140 through 141 removed outlier: 4.056A pdb=" N PHE B 140 " --> pdb=" O ARG B 158 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG B 158 " --> pdb=" O PHE B 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.007A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 612 " --> pdb=" O CYS B 649 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N CYS B 649 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY B 648 " --> pdb=" O THR B 645 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.953A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE B 402 " --> pdb=" O TYR B 508 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 453 through 454 removed outlier: 4.808A pdb=" N TYR B 453 " --> pdb=" O GLN B 493 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N GLN B 493 " --> pdb=" O TYR B 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.149A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.644A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B1056 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 733 through 735 removed outlier: 4.090A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 859 " --> pdb=" O SER B 735 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 787 through 788 Processing sheet with id=AC9, first strand: chain 'B' and resid 1120 through 1121 Processing sheet with id=AD1, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD2, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.746A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 60 through 65 current: chain 'C' and resid 189 through 197 removed outlier: 4.324A pdb=" N VAL C 193 " --> pdb=" O TYR C 204 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR C 204 " --> pdb=" O VAL C 193 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS C 195 " --> pdb=" O LYS C 202 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LYS C 202 " --> pdb=" O LYS C 195 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE C 197 " --> pdb=" O TYR C 200 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.823A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE C 55 " --> pdb=" O GLN C 271 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS C 278 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.914A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP C 104 " --> pdb=" O ILE C 119 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE C 119 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 313 through 318 removed outlier: 6.582A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER C 316 " --> pdb=" O VAL C 595 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR C 612 " --> pdb=" O CYS C 649 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N CYS C 649 " --> pdb=" O TYR C 612 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 325 through 328 removed outlier: 3.578A pdb=" N ILE C 326 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ASN C 542 " --> pdb=" O ILE C 326 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ARG C 328 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 356 through 358 Processing sheet with id=AD8, first strand: chain 'C' and resid 399 through 402 Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.810A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA C 672 " --> pdb=" O ILE C 664 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE C 664 " --> pdb=" O ALA C 672 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 712 through 713 Processing sheet with id=AE3, first strand: chain 'C' and resid 717 through 719 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 717 through 719 current: chain 'C' and resid 1059 through 1070 No H-bonds generated for sheet with id=AE3 Processing sheet with id=AE4, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.213A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR C 859 " --> pdb=" O SER C 735 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1120 through 1122 removed outlier: 3.581A pdb=" N PHE C1121 " --> pdb=" O PHE C1089 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1094 through 1097 removed outlier: 3.570A pdb=" N VAL C1094 " --> pdb=" O THR C1105 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 17 through 23 removed outlier: 3.656A pdb=" N SER D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER D 66 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 46 through 49 removed outlier: 3.592A pdb=" N GLN D 38 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU D 48 " --> pdb=" O TRP D 36 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLY D 98 " --> pdb=" O ASP D 93 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 125 through 129 removed outlier: 3.696A pdb=" N SER D 148 " --> pdb=" O SER D 125 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL D 144 " --> pdb=" O PHE D 129 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA D 141 " --> pdb=" O LEU D 191 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE D 147 " --> pdb=" O ALA D 185 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP D 149 " --> pdb=" O TYR D 183 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N TYR D 183 " --> pdb=" O ASP D 149 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 159 through 160 removed outlier: 4.001A pdb=" N LYS D 160 " --> pdb=" O SER D 203 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER D 203 " --> pdb=" O LYS D 160 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'D' and resid 206 through 207 removed outlier: 4.635A pdb=" N VAL D 206 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL D 213 " --> pdb=" O VAL D 206 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AF4, first strand: chain 'E' and resid 17 through 23 removed outlier: 3.654A pdb=" N MET E 81 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR E 69 " --> pdb=" O GLU E 82 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 45 through 51 removed outlier: 6.943A pdb=" N TRP E 36 " --> pdb=" O MET E 48 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TRP E 50 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N ILE E 34 " --> pdb=" O TRP E 50 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN E 33 " --> pdb=" O SER E 99 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL E 37 " --> pdb=" O PHE E 95 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.660A pdb=" N LEU E 155 " --> pdb=" O PHE E 136 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER E 194 " --> pdb=" O CYS E 154 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR E 190 " --> pdb=" O ASP E 158 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 165 through 168 removed outlier: 3.584A pdb=" N CYS E 210 " --> pdb=" O LYS E 223 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS E 223 " --> pdb=" O CYS E 210 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 9 through 11 removed outlier: 3.897A pdb=" N THR M 108 " --> pdb=" O ALA M 10 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'M' and resid 18 through 23 removed outlier: 3.771A pdb=" N SER M 71 " --> pdb=" O SER M 68 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER M 66 " --> pdb=" O SER M 73 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'M' and resid 45 through 49 removed outlier: 7.074A pdb=" N TRP M 36 " --> pdb=" O LEU M 48 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLY M 98 " --> pdb=" O ASP M 93 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'M' and resid 125 through 129 removed outlier: 4.109A pdb=" N VAL M 144 " --> pdb=" O PHE M 129 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 142 through 150 current: chain 'M' and resid 183 through 185 Processing sheet with id=AG3, first strand: chain 'M' and resid 157 through 160 removed outlier: 3.640A pdb=" N LYS M 160 " --> pdb=" O SER M 203 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER M 203 " --> pdb=" O LYS M 160 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL M 206 " --> pdb=" O VAL M 213 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL M 213 " --> pdb=" O VAL M 206 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'N' and resid 17 through 23 removed outlier: 3.540A pdb=" N ILE N 76 " --> pdb=" O VAL N 18 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'N' and resid 35 through 39 removed outlier: 6.715A pdb=" N TRP N 36 " --> pdb=" O LEU N 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 45 through 49 current: chain 'N' and resid 99 through 100 Processing sheet with id=AG6, first strand: chain 'N' and resid 125 through 129 removed outlier: 4.081A pdb=" N VAL N 144 " --> pdb=" O PHE N 129 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N CYS N 145 " --> pdb=" O SER N 187 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N SER N 187 " --> pdb=" O CYS N 145 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ILE N 147 " --> pdb=" O ALA N 185 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA N 185 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N ALA N 184 " --> pdb=" O PRO N 175 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER N 186 " --> pdb=" O THR N 173 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'N' and resid 141 through 142 Processing sheet with id=AG8, first strand: chain 'N' and resid 158 through 160 removed outlier: 3.994A pdb=" N LYS N 160 " --> pdb=" O SER N 203 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER N 203 " --> pdb=" O LYS N 160 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Q' and resid 33 through 39 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 46 through 47 current: chain 'Q' and resid 116 through 117 Processing sheet with id=AH1, first strand: chain 'Q' and resid 68 through 71 removed outlier: 3.876A pdb=" N GLU Q 82 " --> pdb=" O THR Q 69 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N THR Q 71 " --> pdb=" O TYR Q 80 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N TYR Q 80 " --> pdb=" O THR Q 71 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Q' and resid 150 through 152 removed outlier: 3.592A pdb=" N LEU Q 152 " --> pdb=" O VAL Q 196 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'Q' and resid 165 through 168 removed outlier: 3.566A pdb=" N THR Q 165 " --> pdb=" O ASN Q 213 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS Q 223 " --> pdb=" O CYS Q 210 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL Q 212 " --> pdb=" O VAL Q 221 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL Q 221 " --> pdb=" O VAL Q 212 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N HIS Q 214 " --> pdb=" O THR Q 219 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR Q 219 " --> pdb=" O HIS Q 214 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'R' and resid 33 through 39 removed outlier: 6.761A pdb=" N ILE R 34 " --> pdb=" O TRP R 50 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TRP R 50 " --> pdb=" O ILE R 34 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TRP R 36 " --> pdb=" O MET R 48 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP R 50 " --> pdb=" O ASN R 59 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN R 59 " --> pdb=" O TRP R 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 59 through 60 current: chain 'R' and resid 114 through 117 Processing sheet with id=AH5, first strand: chain 'R' and resid 68 through 72 Processing sheet with id=AH6, first strand: chain 'R' and resid 135 through 137 Processing sheet with id=AH7, first strand: chain 'R' and resid 165 through 168 removed outlier: 4.245A pdb=" N VAL R 212 " --> pdb=" O VAL R 221 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL R 221 " --> pdb=" O VAL R 212 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N HIS R 214 " --> pdb=" O THR R 219 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N THR R 219 " --> pdb=" O HIS R 214 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2400 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.09 Time building geometry restraints manager: 13.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10669 1.34 - 1.47: 8890 1.47 - 1.60: 14918 1.60 - 1.73: 0 1.73 - 1.85: 180 Bond restraints: 34657 Sorted by residual: bond pdb=" C1 NAG B1306 " pdb=" O5 NAG B1306 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.28e+01 bond pdb=" CA ARG B1039 " pdb=" C ARG B1039 " ideal model delta sigma weight residual 1.523 1.487 0.036 1.23e-02 6.61e+03 8.64e+00 bond pdb=" N LYS B1038 " pdb=" CA LYS B1038 " ideal model delta sigma weight residual 1.459 1.424 0.035 1.25e-02 6.40e+03 7.78e+00 bond pdb=" CA ASP B1041 " pdb=" C ASP B1041 " ideal model delta sigma weight residual 1.525 1.487 0.038 1.40e-02 5.10e+03 7.46e+00 bond pdb=" CA SER B1037 " pdb=" C SER B1037 " ideal model delta sigma weight residual 1.523 1.494 0.029 1.21e-02 6.83e+03 5.77e+00 ... (remaining 34652 not shown) Histogram of bond angle deviations from ideal: 98.01 - 105.23: 760 105.23 - 112.44: 17653 112.44 - 119.66: 11169 119.66 - 126.88: 17165 126.88 - 134.09: 442 Bond angle restraints: 47189 Sorted by residual: angle pdb=" C PHE B1042 " pdb=" N CYS B1043 " pdb=" CA CYS B1043 " ideal model delta sigma weight residual 122.95 115.65 7.30 1.44e+00 4.82e-01 2.57e+01 angle pdb=" N SER B1037 " pdb=" CA SER B1037 " pdb=" C SER B1037 " ideal model delta sigma weight residual 108.02 116.80 -8.78 1.75e+00 3.27e-01 2.52e+01 angle pdb=" C VAL A1040 " pdb=" N ASP A1041 " pdb=" CA ASP A1041 " ideal model delta sigma weight residual 121.54 131.00 -9.46 1.91e+00 2.74e-01 2.45e+01 angle pdb=" N LYS B1038 " pdb=" CA LYS B1038 " pdb=" C LYS B1038 " ideal model delta sigma weight residual 111.71 106.03 5.68 1.15e+00 7.56e-01 2.44e+01 angle pdb=" C ASN B1074 " pdb=" CA ASN B1074 " pdb=" CB ASN B1074 " ideal model delta sigma weight residual 109.53 117.43 -7.90 1.65e+00 3.67e-01 2.29e+01 ... (remaining 47184 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 19264 17.91 - 35.82: 1638 35.82 - 53.73: 262 53.73 - 71.65: 90 71.65 - 89.56: 52 Dihedral angle restraints: 21306 sinusoidal: 8877 harmonic: 12429 Sorted by residual: dihedral pdb=" CB CYS C 662 " pdb=" SG CYS C 662 " pdb=" SG CYS C 671 " pdb=" CB CYS C 671 " ideal model delta sinusoidal sigma weight residual -86.00 2.99 -88.99 1 1.00e+01 1.00e-02 9.43e+01 dihedral pdb=" CB CYS B 291 " pdb=" SG CYS B 291 " pdb=" SG CYS B 301 " pdb=" CB CYS B 301 " ideal model delta sinusoidal sigma weight residual -86.00 2.93 -88.93 1 1.00e+01 1.00e-02 9.42e+01 dihedral pdb=" CB CYS A 291 " pdb=" SG CYS A 291 " pdb=" SG CYS A 301 " pdb=" CB CYS A 301 " ideal model delta sinusoidal sigma weight residual 93.00 5.05 87.95 1 1.00e+01 1.00e-02 9.26e+01 ... (remaining 21303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 5447 0.140 - 0.280: 30 0.280 - 0.420: 7 0.420 - 0.560: 1 0.560 - 0.700: 1 Chirality restraints: 5486 Sorted by residual: 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 -1.70 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 122 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.86 -0.54 2.00e-01 2.50e+01 7.35e+00 chirality pdb=" C1 NAG A1310 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A1310 " pdb=" O5 NAG A1310 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.86e+00 ... (remaining 5483 not shown) Planarity restraints: 6040 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B1074 " 0.009 2.00e-02 2.50e+03 3.77e-02 1.77e+01 pdb=" CG ASN B1074 " -0.051 2.00e-02 2.50e+03 pdb=" OD1 ASN B1074 " 0.044 2.00e-02 2.50e+03 pdb=" ND2 ASN B1074 " -0.035 2.00e-02 2.50e+03 pdb=" C1 NAG B1306 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " 0.066 5.00e-02 4.00e+02 9.78e-02 1.53e+01 pdb=" N PRO B 987 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE Q 160 " -0.046 5.00e-02 4.00e+02 6.96e-02 7.75e+00 pdb=" N PRO Q 161 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO Q 161 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO Q 161 " -0.036 5.00e-02 4.00e+02 ... (remaining 6037 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 251 2.57 - 3.15: 24528 3.15 - 3.73: 49741 3.73 - 4.32: 65303 4.32 - 4.90: 108806 Nonbonded interactions: 248629 Sorted by model distance: nonbonded pdb=" CB SER Q 126 " pdb=" CE2 PHE Q 160 " model vdw 1.984 3.740 nonbonded pdb=" CB SER Q 126 " pdb=" CZ PHE Q 160 " model vdw 2.262 3.740 nonbonded pdb=" OG1 THR C 716 " pdb=" OE1 GLN C1071 " model vdw 2.267 2.440 nonbonded pdb=" OG1 THR B 108 " pdb=" O ASN B 234 " model vdw 2.282 2.440 nonbonded pdb=" O ASP A 294 " pdb=" OG SER A 297 " model vdw 2.292 2.440 ... (remaining 248624 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 27 through 142 or resid 155 through 210 or resid 216 throu \ gh 245 or resid 263 through 1147 or resid 1301 through 1309)) selection = (chain 'B' and (resid 27 through 95 or resid 100 through 245 or resid 263 throug \ h 1147 or resid 1301 through 1309)) selection = (chain 'C' and (resid 27 through 142 or resid 155 through 210 or resid 216 throu \ gh 245 or resid 263 through 1147 or resid 1301 through 1309)) } ncs_group { reference = chain 'D' selection = chain 'M' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'O' selection = chain 'P' selection = chain 'S' selection = chain 'T' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.190 Check model and map are aligned: 0.240 Set scattering table: 0.310 Process input model: 82.920 Find NCS groups from input model: 3.830 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 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 0.071 34657 Z= 0.232 Angle : 0.686 12.157 47189 Z= 0.354 Chirality : 0.051 0.700 5486 Planarity : 0.005 0.098 6001 Dihedral : 13.975 89.558 13153 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.98 % Favored : 95.97 % Rotamer: Outliers : 0.16 % Allowed : 0.32 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.49 (0.12), residues: 4192 helix: 0.18 (0.19), residues: 625 sheet: 0.05 (0.18), residues: 819 loop : -1.70 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP Q 113 HIS 0.002 0.000 HIS C1048 PHE 0.037 0.001 PHE Q 160 TYR 0.032 0.001 TYR C 453 ARG 0.007 0.000 ARG Q 67 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 379 time to evaluate : 3.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 THR cc_start: 0.8834 (t) cc_final: 0.7996 (m) REVERT: A 655 TYR cc_start: 0.8742 (t80) cc_final: 0.8495 (t80) REVERT: A 953 ASN cc_start: 0.8059 (t0) cc_final: 0.7834 (t0) REVERT: A 1028 LYS cc_start: 0.7871 (mttt) cc_final: 0.7456 (mttm) REVERT: A 1050 MET cc_start: 0.6712 (ptp) cc_final: 0.6402 (ptp) REVERT: B 135 PHE cc_start: 0.7946 (m-80) cc_final: 0.7535 (m-80) REVERT: B 400 PHE cc_start: 0.8025 (p90) cc_final: 0.7306 (p90) REVERT: B 759 PHE cc_start: 0.5120 (m-10) cc_final: 0.4829 (m-10) REVERT: B 1076 THR cc_start: 0.7504 (p) cc_final: 0.7300 (p) REVERT: B 1118 ASP cc_start: 0.8806 (p0) cc_final: 0.8425 (p0) REVERT: C 55 PHE cc_start: 0.7764 (m-80) cc_final: 0.7502 (m-80) REVERT: C 104 TRP cc_start: 0.6815 (m-90) cc_final: 0.6524 (m-90) REVERT: C 275 PHE cc_start: 0.8206 (m-10) cc_final: 0.7430 (m-10) REVERT: C 298 GLU cc_start: 0.8546 (tm-30) cc_final: 0.8228 (tm-30) REVERT: C 302 THR cc_start: 0.8318 (p) cc_final: 0.7952 (p) REVERT: C 455 LEU cc_start: 0.8437 (tp) cc_final: 0.8184 (tp) REVERT: C 465 GLU cc_start: 0.7892 (pt0) cc_final: 0.7662 (pt0) REVERT: C 513 LEU cc_start: 0.8491 (tp) cc_final: 0.7589 (pp) REVERT: C 562 PHE cc_start: 0.8756 (p90) cc_final: 0.8288 (p90) REVERT: C 977 LEU cc_start: 0.7306 (mm) cc_final: 0.7028 (pp) REVERT: C 978 ASN cc_start: 0.6092 (p0) cc_final: 0.5851 (p0) REVERT: C 1050 MET cc_start: 0.8274 (ppp) cc_final: 0.7635 (ppp) REVERT: E 126 SER cc_start: 0.2823 (m) cc_final: 0.2486 (t) REVERT: M 87 TYR cc_start: 0.5706 (m-80) cc_final: 0.5499 (m-80) REVERT: N 22 CYS cc_start: 0.4947 (t) cc_final: 0.4745 (t) REVERT: N 150 PHE cc_start: 0.3882 (p90) cc_final: 0.3635 (p90) REVERT: Q 31 ASP cc_start: 0.8047 (m-30) cc_final: 0.7480 (m-30) REVERT: R 70 MET cc_start: 0.8706 (mpp) cc_final: 0.8329 (mpp) REVERT: R 108 CYS cc_start: 0.4777 (p) cc_final: 0.4511 (p) REVERT: R 190 TYR cc_start: 0.6948 (m-80) cc_final: 0.6232 (m-10) outliers start: 6 outliers final: 0 residues processed: 385 average time/residue: 0.4143 time to fit residues: 276.2598 Evaluate side-chains 272 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 3.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 359 optimal weight: 40.0000 chunk 322 optimal weight: 40.0000 chunk 179 optimal weight: 7.9990 chunk 110 optimal weight: 9.9990 chunk 217 optimal weight: 0.1980 chunk 172 optimal weight: 0.0670 chunk 333 optimal weight: 20.0000 chunk 129 optimal weight: 9.9990 chunk 203 optimal weight: 0.4980 chunk 248 optimal weight: 5.9990 chunk 386 optimal weight: 9.9990 overall best weight: 2.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 751 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 HIS ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 953 ASN ** C 965 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 178 GLN E 6 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN ** M 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN N 52 ASN Q 3 GLN R 65 GLN ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 34657 Z= 0.275 Angle : 0.605 12.232 47189 Z= 0.307 Chirality : 0.046 0.349 5486 Planarity : 0.005 0.081 6001 Dihedral : 5.960 59.602 5612 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 0.19 % Allowed : 6.03 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.09 (0.13), residues: 4192 helix: 1.24 (0.21), residues: 623 sheet: -0.15 (0.17), residues: 945 loop : -1.52 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 113 HIS 0.008 0.001 HIS C1048 PHE 0.021 0.002 PHE A 906 TYR 0.026 0.001 TYR R 159 ARG 0.010 0.001 ARG B1039 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 338 time to evaluate : 3.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.7331 (t80) cc_final: 0.7001 (t80) REVERT: A 655 TYR cc_start: 0.8721 (t80) cc_final: 0.8356 (t80) REVERT: B 135 PHE cc_start: 0.8069 (m-80) cc_final: 0.7550 (m-80) REVERT: B 400 PHE cc_start: 0.7983 (p90) cc_final: 0.7203 (p90) REVERT: B 401 VAL cc_start: 0.8755 (t) cc_final: 0.8262 (p) REVERT: B 498 ARG cc_start: 0.8571 (mpt180) cc_final: 0.8154 (mmt180) REVERT: B 1041 ASP cc_start: 0.8692 (t0) cc_final: 0.7664 (t0) REVERT: C 275 PHE cc_start: 0.8235 (m-10) cc_final: 0.7528 (m-10) REVERT: C 417 ASN cc_start: 0.8309 (p0) cc_final: 0.8104 (p0) REVERT: C 427 ASP cc_start: 0.7070 (p0) cc_final: 0.6818 (p0) REVERT: C 455 LEU cc_start: 0.8681 (tp) cc_final: 0.8373 (tp) REVERT: C 465 GLU cc_start: 0.8079 (pt0) cc_final: 0.7644 (pt0) REVERT: C 562 PHE cc_start: 0.8861 (p90) cc_final: 0.8422 (p90) REVERT: C 697 MET cc_start: 0.8451 (ttm) cc_final: 0.8223 (ttt) REVERT: C 727 LEU cc_start: 0.9030 (mt) cc_final: 0.8780 (mt) REVERT: C 1050 MET cc_start: 0.8880 (ppp) cc_final: 0.8044 (ppp) REVERT: M 87 TYR cc_start: 0.6188 (m-80) cc_final: 0.5970 (m-80) REVERT: N 22 CYS cc_start: 0.4885 (t) cc_final: 0.4489 (t) REVERT: Q 31 ASP cc_start: 0.7984 (m-30) cc_final: 0.7296 (m-30) REVERT: Q 48 MET cc_start: 0.6688 (pmm) cc_final: 0.6038 (pmm) REVERT: Q 183 VAL cc_start: 0.5808 (m) cc_final: 0.5458 (m) REVERT: R 81 MET cc_start: 0.3445 (mpp) cc_final: 0.3051 (mpp) REVERT: R 98 ARG cc_start: 0.7348 (tmm-80) cc_final: 0.6876 (tmm-80) REVERT: R 190 TYR cc_start: 0.7159 (m-80) cc_final: 0.6835 (m-80) outliers start: 7 outliers final: 2 residues processed: 343 average time/residue: 0.4080 time to fit residues: 243.0694 Evaluate side-chains 244 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 242 time to evaluate : 4.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 214 optimal weight: 4.9990 chunk 120 optimal weight: 0.2980 chunk 321 optimal weight: 20.0000 chunk 263 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 387 optimal weight: 10.0000 chunk 418 optimal weight: 20.0000 chunk 345 optimal weight: 8.9990 chunk 384 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 310 optimal weight: 50.0000 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 317 ASN A 751 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 774 GLN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 GLN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN N 38 GLN Q 3 GLN ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 211 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 34657 Z= 0.247 Angle : 0.562 12.502 47189 Z= 0.288 Chirality : 0.045 0.357 5486 Planarity : 0.004 0.078 6001 Dihedral : 5.801 59.701 5612 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 0.03 % Allowed : 3.98 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.08 (0.13), residues: 4192 helix: 1.26 (0.21), residues: 637 sheet: -0.22 (0.17), residues: 952 loop : -1.49 (0.12), residues: 2603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP Q 111 HIS 0.014 0.001 HIS C 954 PHE 0.034 0.002 PHE A 906 TYR 0.025 0.001 TYR C 508 ARG 0.013 0.001 ARG Q 67 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 338 time to evaluate : 3.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 655 TYR cc_start: 0.8899 (t80) cc_final: 0.8333 (t80) REVERT: B 135 PHE cc_start: 0.8116 (m-80) cc_final: 0.7636 (m-80) REVERT: B 400 PHE cc_start: 0.7964 (p90) cc_final: 0.7029 (p90) REVERT: B 498 ARG cc_start: 0.8530 (mpt180) cc_final: 0.7926 (mpt180) REVERT: B 562 PHE cc_start: 0.7622 (p90) cc_final: 0.7396 (p90) REVERT: B 655 TYR cc_start: 0.8576 (t80) cc_final: 0.8297 (t80) REVERT: B 660 TYR cc_start: 0.6733 (m-10) cc_final: 0.6482 (m-10) REVERT: B 786 LYS cc_start: 0.8743 (mmmt) cc_final: 0.8455 (mtpt) REVERT: B 984 LEU cc_start: 0.8170 (tp) cc_final: 0.7851 (tp) REVERT: B 1029 MET cc_start: 0.7895 (tpp) cc_final: 0.7691 (tpp) REVERT: B 1041 ASP cc_start: 0.8885 (t0) cc_final: 0.8184 (t0) REVERT: C 275 PHE cc_start: 0.8478 (m-10) cc_final: 0.8014 (m-10) REVERT: C 417 ASN cc_start: 0.8302 (p0) cc_final: 0.8088 (p0) REVERT: C 427 ASP cc_start: 0.7133 (p0) cc_final: 0.6816 (p0) REVERT: C 455 LEU cc_start: 0.8657 (tp) cc_final: 0.8379 (tp) REVERT: C 562 PHE cc_start: 0.8758 (p90) cc_final: 0.8317 (p90) REVERT: C 697 MET cc_start: 0.8491 (ttm) cc_final: 0.8245 (ttt) REVERT: C 712 ILE cc_start: 0.8763 (tt) cc_final: 0.8551 (tt) REVERT: C 752 LEU cc_start: 0.8797 (pp) cc_final: 0.8514 (tp) REVERT: C 1050 MET cc_start: 0.8709 (ppp) cc_final: 0.7959 (ppp) REVERT: C 1110 TYR cc_start: 0.8240 (t80) cc_final: 0.7936 (t80) REVERT: N 22 CYS cc_start: 0.4838 (t) cc_final: 0.4530 (t) REVERT: N 35 TYR cc_start: 0.8328 (m-10) cc_final: 0.8104 (m-80) REVERT: Q 31 ASP cc_start: 0.8021 (m-30) cc_final: 0.7391 (m-30) REVERT: Q 48 MET cc_start: 0.6468 (pmm) cc_final: 0.5729 (pmm) REVERT: Q 183 VAL cc_start: 0.5879 (m) cc_final: 0.5594 (m) REVERT: R 81 MET cc_start: 0.3451 (mpp) cc_final: 0.3022 (mpp) REVERT: R 95 PHE cc_start: 0.6925 (m-80) cc_final: 0.6637 (m-80) REVERT: R 190 TYR cc_start: 0.7095 (m-80) cc_final: 0.6811 (m-10) outliers start: 1 outliers final: 0 residues processed: 339 average time/residue: 0.3957 time to fit residues: 228.6022 Evaluate side-chains 233 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 233 time to evaluate : 3.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 382 optimal weight: 20.0000 chunk 291 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 184 optimal weight: 4.9990 chunk 260 optimal weight: 6.9990 chunk 388 optimal weight: 30.0000 chunk 411 optimal weight: 2.9990 chunk 203 optimal weight: 0.0670 chunk 368 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A1054 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 949 GLN B 955 ASN B1083 HIS B1088 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 394 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 954 HIS ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN M 137 GLN ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 34657 Z= 0.262 Angle : 0.573 9.948 47189 Z= 0.292 Chirality : 0.045 0.347 5486 Planarity : 0.004 0.080 6001 Dihedral : 5.826 59.163 5612 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.05 % Allowed : 3.90 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.12 (0.13), residues: 4192 helix: 1.17 (0.21), residues: 644 sheet: -0.26 (0.16), residues: 956 loop : -1.51 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 886 HIS 0.009 0.001 HIS C 954 PHE 0.022 0.002 PHE B1042 TYR 0.018 0.001 TYR R 102 ARG 0.006 0.000 ARG A1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 314 time to evaluate : 3.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.7048 (t80) cc_final: 0.6755 (t80) REVERT: A 655 TYR cc_start: 0.8991 (t80) cc_final: 0.8254 (t80) REVERT: A 1050 MET cc_start: 0.7581 (ptp) cc_final: 0.7035 (ptp) REVERT: B 135 PHE cc_start: 0.7971 (m-80) cc_final: 0.7766 (m-80) REVERT: B 371 PHE cc_start: 0.5954 (t80) cc_final: 0.5672 (t80) REVERT: B 378 LYS cc_start: 0.8089 (mmtt) cc_final: 0.7704 (tmtt) REVERT: B 400 PHE cc_start: 0.7948 (p90) cc_final: 0.6951 (p90) REVERT: B 498 ARG cc_start: 0.8650 (mpt180) cc_final: 0.7933 (mpt180) REVERT: B 655 TYR cc_start: 0.8681 (t80) cc_final: 0.8223 (t80) REVERT: B 660 TYR cc_start: 0.6658 (m-10) cc_final: 0.6231 (m-10) REVERT: B 902 MET cc_start: 0.8785 (mmt) cc_final: 0.8537 (mpp) REVERT: B 950 ASP cc_start: 0.8650 (t0) cc_final: 0.8343 (t0) REVERT: B 1029 MET cc_start: 0.7631 (tpp) cc_final: 0.7327 (tpp) REVERT: B 1041 ASP cc_start: 0.9279 (t0) cc_final: 0.8353 (t0) REVERT: C 390 LEU cc_start: 0.8265 (mt) cc_final: 0.8063 (mt) REVERT: C 427 ASP cc_start: 0.7089 (p0) cc_final: 0.6847 (p0) REVERT: C 455 LEU cc_start: 0.8684 (tp) cc_final: 0.8379 (tp) REVERT: C 562 PHE cc_start: 0.8804 (p90) cc_final: 0.8399 (p90) REVERT: C 697 MET cc_start: 0.8501 (ttm) cc_final: 0.8210 (ttt) REVERT: C 1050 MET cc_start: 0.8912 (ppp) cc_final: 0.8614 (ppp) REVERT: C 1110 TYR cc_start: 0.8344 (t80) cc_final: 0.8086 (t80) REVERT: M 35 TYR cc_start: 0.5755 (m-10) cc_final: 0.5554 (m-10) REVERT: M 88 TYR cc_start: 0.6327 (m-80) cc_final: 0.5362 (m-80) REVERT: N 22 CYS cc_start: 0.5513 (t) cc_final: 0.5137 (t) REVERT: Q 29 PHE cc_start: 0.8348 (t80) cc_final: 0.7609 (t80) REVERT: Q 31 ASP cc_start: 0.8045 (m-30) cc_final: 0.7481 (m-30) REVERT: Q 72 ARG cc_start: 0.6619 (mtt-85) cc_final: 0.5541 (ttm-80) REVERT: Q 111 TRP cc_start: 0.8048 (m-10) cc_final: 0.7756 (m-10) REVERT: Q 183 VAL cc_start: 0.5914 (m) cc_final: 0.5605 (m) REVERT: R 95 PHE cc_start: 0.7044 (m-80) cc_final: 0.6678 (m-80) REVERT: R 190 TYR cc_start: 0.6982 (m-80) cc_final: 0.6764 (m-10) outliers start: 2 outliers final: 1 residues processed: 315 average time/residue: 0.4203 time to fit residues: 226.2652 Evaluate side-chains 237 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 236 time to evaluate : 4.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 342 optimal weight: 5.9990 chunk 233 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 306 optimal weight: 8.9990 chunk 169 optimal weight: 0.0670 chunk 351 optimal weight: 0.0020 chunk 284 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 210 optimal weight: 3.9990 chunk 369 optimal weight: 9.9990 chunk 103 optimal weight: 0.4980 overall best weight: 1.9130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 644 GLN A 751 ASN ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN ** C 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 ASN ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34657 Z= 0.185 Angle : 0.521 10.805 47189 Z= 0.263 Chirality : 0.045 0.352 5486 Planarity : 0.004 0.079 6001 Dihedral : 5.533 57.239 5612 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 0.03 % Allowed : 2.37 % Favored : 97.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.02 (0.13), residues: 4192 helix: 1.48 (0.21), residues: 631 sheet: -0.19 (0.17), residues: 937 loop : -1.49 (0.12), residues: 2624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 353 HIS 0.005 0.001 HIS B1088 PHE 0.015 0.001 PHE R 180 TYR 0.020 0.001 TYR C 508 ARG 0.005 0.000 ARG Q 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 325 time to evaluate : 3.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.7136 (t80) cc_final: 0.6855 (t80) REVERT: A 655 TYR cc_start: 0.8994 (t80) cc_final: 0.8256 (t80) REVERT: A 858 LEU cc_start: 0.8935 (mm) cc_final: 0.8659 (mm) REVERT: B 135 PHE cc_start: 0.7859 (m-80) cc_final: 0.7589 (m-80) REVERT: B 371 PHE cc_start: 0.6057 (t80) cc_final: 0.5820 (t80) REVERT: B 442 ASP cc_start: 0.7887 (t0) cc_final: 0.7488 (t70) REVERT: B 498 ARG cc_start: 0.8480 (mpt180) cc_final: 0.7501 (mpt180) REVERT: B 655 TYR cc_start: 0.8675 (t80) cc_final: 0.8126 (t80) REVERT: B 660 TYR cc_start: 0.6731 (m-10) cc_final: 0.6269 (m-10) REVERT: B 786 LYS cc_start: 0.8629 (mmmt) cc_final: 0.8400 (mtpt) REVERT: B 1029 MET cc_start: 0.7652 (tpp) cc_final: 0.7360 (tpp) REVERT: B 1041 ASP cc_start: 0.9288 (t0) cc_final: 0.8327 (t0) REVERT: C 56 LEU cc_start: 0.8514 (tp) cc_final: 0.8261 (tp) REVERT: C 427 ASP cc_start: 0.7166 (p0) cc_final: 0.6886 (p0) REVERT: C 429 PHE cc_start: 0.7523 (t80) cc_final: 0.7229 (t80) REVERT: C 455 LEU cc_start: 0.8836 (tp) cc_final: 0.8552 (tp) REVERT: C 562 PHE cc_start: 0.8697 (p90) cc_final: 0.8278 (p90) REVERT: C 697 MET cc_start: 0.8523 (ttm) cc_final: 0.8260 (ttt) REVERT: C 752 LEU cc_start: 0.8576 (pp) cc_final: 0.8354 (tp) REVERT: C 1110 TYR cc_start: 0.8333 (t80) cc_final: 0.8026 (t80) REVERT: M 87 TYR cc_start: 0.6101 (m-80) cc_final: 0.5781 (m-80) REVERT: M 88 TYR cc_start: 0.6105 (m-80) cc_final: 0.5521 (m-80) REVERT: N 22 CYS cc_start: 0.5516 (t) cc_final: 0.5158 (t) REVERT: Q 29 PHE cc_start: 0.8298 (t80) cc_final: 0.7523 (t80) REVERT: Q 31 ASP cc_start: 0.8082 (m-30) cc_final: 0.7522 (m-30) REVERT: Q 70 MET cc_start: 0.2543 (mpp) cc_final: 0.0717 (tpt) REVERT: Q 72 ARG cc_start: 0.5833 (ttm-80) cc_final: 0.5340 (ttm-80) REVERT: Q 111 TRP cc_start: 0.8062 (m-10) cc_final: 0.7730 (m-10) REVERT: Q 112 MET cc_start: 0.8806 (ptt) cc_final: 0.8453 (ptp) REVERT: Q 183 VAL cc_start: 0.5954 (m) cc_final: 0.5645 (m) REVERT: R 81 MET cc_start: 0.3540 (mpp) cc_final: 0.3321 (mpp) REVERT: R 95 PHE cc_start: 0.7182 (m-80) cc_final: 0.6785 (m-80) REVERT: R 190 TYR cc_start: 0.6946 (m-80) cc_final: 0.6668 (m-80) outliers start: 1 outliers final: 0 residues processed: 326 average time/residue: 0.4145 time to fit residues: 229.3274 Evaluate side-chains 238 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 138 optimal weight: 3.9990 chunk 370 optimal weight: 0.3980 chunk 81 optimal weight: 9.9990 chunk 241 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 412 optimal weight: 20.0000 chunk 342 optimal weight: 4.9990 chunk 190 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 216 optimal weight: 7.9990 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 777 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 658 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 ASN M 119 GLN ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 39 GLN ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 34657 Z= 0.294 Angle : 0.608 9.849 47189 Z= 0.310 Chirality : 0.046 0.344 5486 Planarity : 0.005 0.082 6001 Dihedral : 5.884 59.641 5612 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.05 % Allowed : 3.12 % Favored : 96.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.23 (0.13), residues: 4192 helix: 1.08 (0.20), residues: 646 sheet: -0.38 (0.17), residues: 937 loop : -1.55 (0.12), residues: 2609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 886 HIS 0.006 0.001 HIS A1064 PHE 0.019 0.002 PHE A 888 TYR 0.018 0.002 TYR C 453 ARG 0.011 0.001 ARG R 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 302 time to evaluate : 3.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.7123 (t80) cc_final: 0.6800 (t80) REVERT: A 655 TYR cc_start: 0.9021 (t80) cc_final: 0.8212 (t80) REVERT: A 858 LEU cc_start: 0.9028 (mm) cc_final: 0.8771 (mm) REVERT: A 1050 MET cc_start: 0.7316 (ptp) cc_final: 0.6827 (ptp) REVERT: B 135 PHE cc_start: 0.7847 (m-80) cc_final: 0.7533 (m-80) REVERT: B 200 TYR cc_start: 0.6214 (m-10) cc_final: 0.5529 (m-80) REVERT: B 498 ARG cc_start: 0.8371 (mpt180) cc_final: 0.7425 (mpt180) REVERT: B 660 TYR cc_start: 0.6741 (m-10) cc_final: 0.6202 (m-10) REVERT: B 902 MET cc_start: 0.8775 (mmt) cc_final: 0.8531 (mpp) REVERT: B 1041 ASP cc_start: 0.9071 (t0) cc_final: 0.8411 (t0) REVERT: C 390 LEU cc_start: 0.8326 (mt) cc_final: 0.8105 (mt) REVERT: C 427 ASP cc_start: 0.6991 (p0) cc_final: 0.6671 (p0) REVERT: C 429 PHE cc_start: 0.7611 (t80) cc_final: 0.7313 (t80) REVERT: C 455 LEU cc_start: 0.8884 (tp) cc_final: 0.8544 (tp) REVERT: C 498 ARG cc_start: 0.7877 (mmp80) cc_final: 0.7587 (mmm160) REVERT: C 562 PHE cc_start: 0.8924 (p90) cc_final: 0.8574 (p90) REVERT: C 697 MET cc_start: 0.8562 (ttm) cc_final: 0.8353 (ttt) REVERT: C 712 ILE cc_start: 0.8900 (tt) cc_final: 0.8649 (tt) REVERT: C 1050 MET cc_start: 0.8917 (ppp) cc_final: 0.8671 (ppp) REVERT: C 1110 TYR cc_start: 0.8363 (t80) cc_final: 0.8045 (t80) REVERT: D 5 THR cc_start: 0.2825 (m) cc_final: 0.2609 (m) REVERT: E 126 SER cc_start: 0.3183 (m) cc_final: 0.2811 (t) REVERT: M 35 TYR cc_start: 0.5358 (m-10) cc_final: 0.4970 (m-10) REVERT: M 87 TYR cc_start: 0.5781 (m-80) cc_final: 0.5451 (m-80) REVERT: N 22 CYS cc_start: 0.5437 (t) cc_final: 0.4985 (t) REVERT: Q 29 PHE cc_start: 0.8356 (t80) cc_final: 0.7542 (t80) REVERT: Q 31 ASP cc_start: 0.8100 (m-30) cc_final: 0.7578 (m-30) REVERT: Q 70 MET cc_start: 0.3652 (mpp) cc_final: 0.1494 (tpt) REVERT: Q 72 ARG cc_start: 0.5840 (ttm-80) cc_final: 0.5443 (mtp85) REVERT: Q 111 TRP cc_start: 0.7922 (m-10) cc_final: 0.7697 (m-10) REVERT: Q 183 VAL cc_start: 0.5975 (m) cc_final: 0.5675 (m) REVERT: R 31 ASP cc_start: 0.7827 (p0) cc_final: 0.7130 (m-30) REVERT: R 32 TYR cc_start: 0.7659 (m-80) cc_final: 0.7338 (m-80) REVERT: R 46 GLU cc_start: 0.8401 (pm20) cc_final: 0.8076 (mp0) REVERT: R 81 MET cc_start: 0.3997 (mpp) cc_final: 0.3671 (mpp) REVERT: R 94 TYR cc_start: 0.7147 (m-80) cc_final: 0.6876 (m-10) REVERT: R 95 PHE cc_start: 0.7211 (m-80) cc_final: 0.6718 (m-80) REVERT: R 190 TYR cc_start: 0.6932 (m-80) cc_final: 0.6632 (m-80) outliers start: 2 outliers final: 1 residues processed: 303 average time/residue: 0.4085 time to fit residues: 211.7134 Evaluate side-chains 229 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 3.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 397 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 234 optimal weight: 7.9990 chunk 300 optimal weight: 6.9990 chunk 233 optimal weight: 9.9990 chunk 346 optimal weight: 20.0000 chunk 230 optimal weight: 1.9990 chunk 410 optimal weight: 8.9990 chunk 256 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 271 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 658 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 54 GLN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 119 GLN N 205 GLN ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 34657 Z= 0.354 Angle : 0.659 9.851 47189 Z= 0.338 Chirality : 0.047 0.352 5486 Planarity : 0.005 0.082 6001 Dihedral : 6.331 59.035 5612 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.03 % Allowed : 2.26 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.45 (0.13), residues: 4192 helix: 0.82 (0.20), residues: 640 sheet: -0.57 (0.17), residues: 929 loop : -1.65 (0.12), residues: 2623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 886 HIS 0.007 0.001 HIS C1083 PHE 0.029 0.002 PHE A 906 TYR 0.030 0.002 TYR E 32 ARG 0.011 0.001 ARG D 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 291 time to evaluate : 3.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.7261 (t80) cc_final: 0.6933 (t80) REVERT: A 655 TYR cc_start: 0.8998 (t80) cc_final: 0.8215 (t80) REVERT: A 858 LEU cc_start: 0.9101 (mm) cc_final: 0.8886 (mm) REVERT: A 1050 MET cc_start: 0.7251 (ptp) cc_final: 0.6762 (ptp) REVERT: B 135 PHE cc_start: 0.7871 (m-80) cc_final: 0.7580 (m-80) REVERT: B 498 ARG cc_start: 0.8052 (mpt180) cc_final: 0.7350 (mpt180) REVERT: B 660 TYR cc_start: 0.6821 (m-10) cc_final: 0.6317 (m-10) REVERT: B 786 LYS cc_start: 0.8607 (mmmt) cc_final: 0.8357 (mtpt) REVERT: B 902 MET cc_start: 0.8784 (mmt) cc_final: 0.8537 (tpp) REVERT: B 1029 MET cc_start: 0.7606 (tpp) cc_final: 0.7390 (tpp) REVERT: B 1031 GLU cc_start: 0.7593 (pt0) cc_final: 0.7168 (pt0) REVERT: B 1041 ASP cc_start: 0.9301 (t0) cc_final: 0.8550 (t0) REVERT: B 1050 MET cc_start: 0.8173 (tpt) cc_final: 0.7488 (tpp) REVERT: C 128 ILE cc_start: 0.7102 (mm) cc_final: 0.6871 (mm) REVERT: C 390 LEU cc_start: 0.8365 (mt) cc_final: 0.8141 (mt) REVERT: C 427 ASP cc_start: 0.6807 (p0) cc_final: 0.6440 (p0) REVERT: C 429 PHE cc_start: 0.7643 (t80) cc_final: 0.7279 (t80) REVERT: C 455 LEU cc_start: 0.8863 (tp) cc_final: 0.8535 (tp) REVERT: C 562 PHE cc_start: 0.8848 (p90) cc_final: 0.8545 (p90) REVERT: C 712 ILE cc_start: 0.8959 (tt) cc_final: 0.8748 (tt) REVERT: C 858 LEU cc_start: 0.8628 (mm) cc_final: 0.8269 (pp) REVERT: C 922 LEU cc_start: 0.9057 (tp) cc_final: 0.8854 (tp) REVERT: C 1110 TYR cc_start: 0.8389 (t80) cc_final: 0.8084 (t80) REVERT: E 126 SER cc_start: 0.3342 (m) cc_final: 0.2975 (t) REVERT: M 87 TYR cc_start: 0.5595 (m-80) cc_final: 0.5264 (m-80) REVERT: N 22 CYS cc_start: 0.5517 (t) cc_final: 0.5236 (t) REVERT: Q 29 PHE cc_start: 0.8458 (t80) cc_final: 0.7507 (t80) REVERT: Q 31 ASP cc_start: 0.8161 (m-30) cc_final: 0.7862 (m-30) REVERT: Q 67 ARG cc_start: 0.6105 (mpp-170) cc_final: 0.5844 (mtm-85) REVERT: Q 72 ARG cc_start: 0.5869 (ttm-80) cc_final: 0.5323 (ttm-80) REVERT: Q 183 VAL cc_start: 0.5942 (m) cc_final: 0.5642 (m) REVERT: R 81 MET cc_start: 0.4234 (mpp) cc_final: 0.3924 (mpp) REVERT: R 95 PHE cc_start: 0.7447 (m-80) cc_final: 0.6898 (m-80) outliers start: 1 outliers final: 0 residues processed: 292 average time/residue: 0.4140 time to fit residues: 206.0850 Evaluate side-chains 222 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 4.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 254 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 245 optimal weight: 5.9990 chunk 123 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 279 optimal weight: 7.9990 chunk 203 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 322 optimal weight: 7.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 271 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 955 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 658 ASN C 777 ASN C 953 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 GLN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34657 Z= 0.176 Angle : 0.545 10.438 47189 Z= 0.276 Chirality : 0.045 0.370 5486 Planarity : 0.004 0.083 6001 Dihedral : 5.776 58.995 5612 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.23 (0.13), residues: 4192 helix: 1.14 (0.20), residues: 649 sheet: -0.41 (0.16), residues: 980 loop : -1.58 (0.12), residues: 2563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP Q 111 HIS 0.006 0.001 HIS C1048 PHE 0.019 0.001 PHE C 58 TYR 0.017 0.001 TYR A 917 ARG 0.011 0.000 ARG C1019 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 3.823 Fit side-chains revert: symmetry clash REVERT: A 429 PHE cc_start: 0.7077 (t80) cc_final: 0.6799 (t80) REVERT: A 655 TYR cc_start: 0.8983 (t80) cc_final: 0.8256 (t80) REVERT: A 858 LEU cc_start: 0.9139 (mm) cc_final: 0.8902 (mm) REVERT: B 135 PHE cc_start: 0.7755 (m-80) cc_final: 0.7522 (m-80) REVERT: B 498 ARG cc_start: 0.8258 (mpt180) cc_final: 0.7346 (mpt180) REVERT: B 777 ASN cc_start: 0.8681 (m-40) cc_final: 0.8240 (m110) REVERT: B 786 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8351 (mtpt) REVERT: B 819 GLU cc_start: 0.8961 (pt0) cc_final: 0.8426 (tt0) REVERT: B 878 LEU cc_start: 0.8785 (mm) cc_final: 0.8489 (mm) REVERT: B 977 LEU cc_start: 0.8349 (mm) cc_final: 0.8138 (mm) REVERT: B 1029 MET cc_start: 0.7567 (tpp) cc_final: 0.7197 (tpp) REVERT: B 1041 ASP cc_start: 0.9252 (t0) cc_final: 0.8462 (t0) REVERT: B 1067 TYR cc_start: 0.7755 (t80) cc_final: 0.7360 (t80) REVERT: C 40 ASP cc_start: 0.8765 (p0) cc_final: 0.8291 (p0) REVERT: C 42 VAL cc_start: 0.8329 (t) cc_final: 0.7908 (p) REVERT: C 56 LEU cc_start: 0.8540 (tp) cc_final: 0.8303 (tp) REVERT: C 128 ILE cc_start: 0.7390 (mm) cc_final: 0.7052 (mm) REVERT: C 427 ASP cc_start: 0.7009 (p0) cc_final: 0.6654 (p0) REVERT: C 429 PHE cc_start: 0.7521 (t80) cc_final: 0.7122 (t80) REVERT: C 455 LEU cc_start: 0.8737 (tp) cc_final: 0.8424 (tp) REVERT: C 562 PHE cc_start: 0.8923 (p90) cc_final: 0.8632 (p90) REVERT: C 752 LEU cc_start: 0.8627 (pp) cc_final: 0.8282 (tp) REVERT: C 858 LEU cc_start: 0.8700 (mm) cc_final: 0.8331 (pp) REVERT: C 1110 TYR cc_start: 0.8359 (t80) cc_final: 0.8086 (t80) REVERT: E 126 SER cc_start: 0.3274 (m) cc_final: 0.2921 (t) REVERT: M 35 TYR cc_start: 0.5408 (m-10) cc_final: 0.4912 (m-10) REVERT: M 87 TYR cc_start: 0.5784 (m-80) cc_final: 0.5512 (m-80) REVERT: N 22 CYS cc_start: 0.5276 (t) cc_final: 0.4929 (t) REVERT: N 47 LEU cc_start: 0.9126 (pt) cc_final: 0.8807 (pp) REVERT: N 63 PHE cc_start: 0.7099 (m-10) cc_final: 0.6878 (m-80) REVERT: Q 29 PHE cc_start: 0.8375 (t80) cc_final: 0.7395 (t80) REVERT: Q 31 ASP cc_start: 0.8198 (m-30) cc_final: 0.7864 (m-30) REVERT: Q 72 ARG cc_start: 0.6221 (ttm-80) cc_final: 0.5935 (mtp85) REVERT: Q 112 MET cc_start: 0.7989 (ptp) cc_final: 0.7154 (ptp) REVERT: Q 183 VAL cc_start: 0.6043 (m) cc_final: 0.5781 (m) REVERT: R 37 VAL cc_start: 0.9179 (p) cc_final: 0.8942 (t) REVERT: R 81 MET cc_start: 0.4170 (mpp) cc_final: 0.3818 (mpp) REVERT: R 95 PHE cc_start: 0.7271 (m-80) cc_final: 0.6725 (m-80) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.4107 time to fit residues: 222.2249 Evaluate side-chains 237 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 237 time to evaluate : 3.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 373 optimal weight: 10.0000 chunk 393 optimal weight: 9.9990 chunk 358 optimal weight: 30.0000 chunk 382 optimal weight: 0.6980 chunk 230 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 300 optimal weight: 30.0000 chunk 117 optimal weight: 2.9990 chunk 345 optimal weight: 7.9990 chunk 361 optimal weight: 10.0000 chunk 381 optimal weight: 9.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 271 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 955 ASN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1048 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 505 HIS C 658 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 34657 Z= 0.276 Angle : 0.600 9.842 47189 Z= 0.306 Chirality : 0.046 0.361 5486 Planarity : 0.005 0.083 6001 Dihedral : 5.908 57.745 5612 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.23 % Favored : 92.77 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.36 (0.13), residues: 4192 helix: 0.92 (0.20), residues: 654 sheet: -0.52 (0.16), residues: 988 loop : -1.62 (0.12), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP Q 111 HIS 0.005 0.001 HIS C1083 PHE 0.022 0.002 PHE B 371 TYR 0.017 0.001 TYR C 453 ARG 0.006 0.001 ARG C 498 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 304 time to evaluate : 3.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.7062 (t80) cc_final: 0.6842 (t80) REVERT: A 655 TYR cc_start: 0.8966 (t80) cc_final: 0.8179 (t80) REVERT: A 858 LEU cc_start: 0.9175 (mm) cc_final: 0.8946 (mm) REVERT: B 135 PHE cc_start: 0.7793 (m-80) cc_final: 0.7549 (m-80) REVERT: B 498 ARG cc_start: 0.8098 (mpt180) cc_final: 0.7175 (mpt180) REVERT: B 777 ASN cc_start: 0.8777 (m-40) cc_final: 0.8286 (m110) REVERT: B 902 MET cc_start: 0.8675 (tpp) cc_final: 0.8407 (mpp) REVERT: B 977 LEU cc_start: 0.8362 (mm) cc_final: 0.8147 (mm) REVERT: B 1029 MET cc_start: 0.7540 (tpp) cc_final: 0.7324 (tpp) REVERT: B 1031 GLU cc_start: 0.7722 (pt0) cc_final: 0.7313 (pt0) REVERT: B 1041 ASP cc_start: 0.9103 (t0) cc_final: 0.8406 (t0) REVERT: B 1050 MET cc_start: 0.7926 (tpp) cc_final: 0.7407 (tpp) REVERT: B 1067 TYR cc_start: 0.7982 (t80) cc_final: 0.7655 (t80) REVERT: C 427 ASP cc_start: 0.6955 (p0) cc_final: 0.6491 (p0) REVERT: C 429 PHE cc_start: 0.7551 (t80) cc_final: 0.7119 (t80) REVERT: C 455 LEU cc_start: 0.8776 (tp) cc_final: 0.8468 (tp) REVERT: C 562 PHE cc_start: 0.8961 (p90) cc_final: 0.8699 (p90) REVERT: C 712 ILE cc_start: 0.8934 (tt) cc_final: 0.8699 (tt) REVERT: C 752 LEU cc_start: 0.8699 (pp) cc_final: 0.8188 (tp) REVERT: C 755 GLN cc_start: 0.8413 (mt0) cc_final: 0.7999 (mt0) REVERT: C 858 LEU cc_start: 0.8671 (mm) cc_final: 0.8377 (pp) REVERT: C 900 MET cc_start: 0.7548 (mmp) cc_final: 0.7301 (mmm) REVERT: C 1050 MET cc_start: 0.8778 (ppp) cc_final: 0.8065 (ppp) REVERT: C 1110 TYR cc_start: 0.8363 (t80) cc_final: 0.8139 (t80) REVERT: E 126 SER cc_start: 0.3345 (m) cc_final: 0.2993 (t) REVERT: M 87 TYR cc_start: 0.5630 (m-80) cc_final: 0.5336 (m-80) REVERT: N 22 CYS cc_start: 0.5416 (t) cc_final: 0.5117 (t) REVERT: Q 29 PHE cc_start: 0.8408 (t80) cc_final: 0.7436 (t80) REVERT: Q 31 ASP cc_start: 0.8292 (m-30) cc_final: 0.8014 (m-30) REVERT: Q 112 MET cc_start: 0.7980 (ptp) cc_final: 0.6826 (ptp) REVERT: Q 183 VAL cc_start: 0.6002 (m) cc_final: 0.5721 (m) REVERT: R 36 TRP cc_start: 0.8267 (m100) cc_final: 0.7221 (m100) REVERT: R 160 PHE cc_start: 0.4756 (m-10) cc_final: 0.4439 (m-10) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.3983 time to fit residues: 208.1023 Evaluate side-chains 212 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 4.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 251 optimal weight: 0.5980 chunk 404 optimal weight: 6.9990 chunk 246 optimal weight: 0.9990 chunk 191 optimal weight: 4.9990 chunk 281 optimal weight: 10.0000 chunk 424 optimal weight: 10.0000 chunk 390 optimal weight: 20.0000 chunk 337 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 207 optimal weight: 0.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 955 ASN ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 394 ASN C 658 ASN C 777 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.4059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 34657 Z= 0.206 Angle : 0.563 10.193 47189 Z= 0.285 Chirality : 0.046 0.453 5486 Planarity : 0.004 0.083 6001 Dihedral : 5.729 58.253 5612 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.29 (0.13), residues: 4192 helix: 1.11 (0.21), residues: 648 sheet: -0.49 (0.16), residues: 998 loop : -1.60 (0.12), residues: 2546 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP Q 111 HIS 0.003 0.001 HIS C 49 PHE 0.021 0.001 PHE B 371 TYR 0.014 0.001 TYR A 917 ARG 0.005 0.000 ARG C 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8384 Ramachandran restraints generated. 4192 Oldfield, 0 Emsley, 4192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 300 time to evaluate : 3.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 429 PHE cc_start: 0.6995 (t80) cc_final: 0.6612 (t80) REVERT: A 655 TYR cc_start: 0.8959 (t80) cc_final: 0.8210 (t80) REVERT: A 858 LEU cc_start: 0.9167 (mm) cc_final: 0.8926 (mm) REVERT: B 135 PHE cc_start: 0.7795 (m-80) cc_final: 0.7556 (m-80) REVERT: B 498 ARG cc_start: 0.8079 (mpt180) cc_final: 0.7172 (mpt180) REVERT: B 660 TYR cc_start: 0.6785 (m-10) cc_final: 0.6246 (m-10) REVERT: B 777 ASN cc_start: 0.8712 (m-40) cc_final: 0.8242 (m110) REVERT: B 786 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8334 (mtpt) REVERT: B 902 MET cc_start: 0.8638 (tpp) cc_final: 0.8405 (mpp) REVERT: B 977 LEU cc_start: 0.8410 (mm) cc_final: 0.8189 (mm) REVERT: B 1029 MET cc_start: 0.7696 (tpp) cc_final: 0.7406 (tpp) REVERT: B 1031 GLU cc_start: 0.7669 (pt0) cc_final: 0.7248 (pt0) REVERT: B 1036 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8238 (tm-30) REVERT: B 1041 ASP cc_start: 0.9158 (t0) cc_final: 0.8361 (t0) REVERT: B 1050 MET cc_start: 0.7879 (tpp) cc_final: 0.7378 (tpp) REVERT: B 1067 TYR cc_start: 0.7865 (t80) cc_final: 0.7631 (t80) REVERT: C 427 ASP cc_start: 0.6910 (p0) cc_final: 0.6515 (p0) REVERT: C 429 PHE cc_start: 0.7608 (t80) cc_final: 0.7183 (t80) REVERT: C 455 LEU cc_start: 0.8741 (tp) cc_final: 0.8478 (tp) REVERT: C 712 ILE cc_start: 0.8942 (tt) cc_final: 0.8668 (tt) REVERT: C 752 LEU cc_start: 0.8691 (pp) cc_final: 0.8393 (tp) REVERT: C 858 LEU cc_start: 0.8649 (mm) cc_final: 0.8347 (pp) REVERT: C 900 MET cc_start: 0.7686 (mmp) cc_final: 0.7211 (tpp) REVERT: C 1110 TYR cc_start: 0.8336 (t80) cc_final: 0.8119 (t80) REVERT: E 126 SER cc_start: 0.3423 (m) cc_final: 0.3094 (t) REVERT: M 87 TYR cc_start: 0.5599 (m-80) cc_final: 0.5312 (m-80) REVERT: N 22 CYS cc_start: 0.5406 (t) cc_final: 0.5063 (t) REVERT: Q 29 PHE cc_start: 0.8304 (t80) cc_final: 0.7502 (t80) REVERT: Q 31 ASP cc_start: 0.8433 (m-30) cc_final: 0.7993 (m-30) REVERT: Q 72 ARG cc_start: 0.6305 (ttm-80) cc_final: 0.5921 (ttm-80) REVERT: Q 112 MET cc_start: 0.7978 (ptp) cc_final: 0.6858 (ptp) REVERT: R 36 TRP cc_start: 0.8173 (m100) cc_final: 0.7251 (m100) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.4043 time to fit residues: 209.5658 Evaluate side-chains 222 residues out of total 3716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 222 time to evaluate : 3.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 426 random chunks: chunk 268 optimal weight: 0.0010 chunk 360 optimal weight: 7.9990 chunk 103 optimal weight: 0.7980 chunk 311 optimal weight: 40.0000 chunk 49 optimal weight: 10.0000 chunk 93 optimal weight: 0.3980 chunk 338 optimal weight: 2.9990 chunk 141 optimal weight: 0.0980 chunk 347 optimal weight: 50.0000 chunk 42 optimal weight: 0.0980 chunk 62 optimal weight: 0.0470 overall best weight: 0.1284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 GLN ** A 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A 955 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 417 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 774 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 658 ASN C 777 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 195 GLN ** M 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.112914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.081073 restraints weight = 126401.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.081480 restraints weight = 83803.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.081862 restraints weight = 64328.438| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34657 Z= 0.133 Angle : 0.524 11.067 47189 Z= 0.262 Chirality : 0.045 0.385 5486 Planarity : 0.004 0.080 6001 Dihedral : 5.069 58.585 5612 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % 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: -1.06 (0.13), residues: 4192 helix: 1.43 (0.21), residues: 647 sheet: -0.27 (0.17), residues: 952 loop : -1.50 (0.12), residues: 2593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP Q 111 HIS 0.008 0.001 HIS C1048 PHE 0.018 0.001 PHE C 58 TYR 0.025 0.001 TYR E 32 ARG 0.005 0.000 ARG B1039 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5826.44 seconds wall clock time: 106 minutes 31.38 seconds (6391.38 seconds total)