Starting phenix.real_space_refine on Tue Mar 19 17:18:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb3_31050/03_2024/7eb3_31050.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb3_31050/03_2024/7eb3_31050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb3_31050/03_2024/7eb3_31050.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb3_31050/03_2024/7eb3_31050.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb3_31050/03_2024/7eb3_31050.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eb3_31050/03_2024/7eb3_31050.pdb" } resolution = 3.6 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= 0.042 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 105 5.16 5 C 15799 2.51 5 N 4023 2.21 5 O 4917 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 24844 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 7879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1010, 7879 Classifications: {'peptide': 1010} Link IDs: {'PTRANS': 50, 'TRANS': 959} Chain breaks: 7 Chain: "B" Number of atoms: 7935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1016, 7935 Classifications: {'peptide': 1016} Link IDs: {'PTRANS': 51, 'TRANS': 964} Chain breaks: 7 Chain: "C" Number of atoms: 7927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1015, 7927 Classifications: {'peptide': 1015} Link IDs: {'PTRANS': 51, 'TRANS': 963} Chain breaks: 7 Chain: "D" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" 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: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 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: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: "A" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 70 Unusual residues: {'NAG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 12.85, per 1000 atoms: 0.52 Number of scatterers: 24844 At special positions: 0 Unit cell: (137.5, 141.9, 200.2, 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 105 16.00 O 4917 8.00 N 4023 7.00 C 15799 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=34, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " 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=2.04 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 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 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.04 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " 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 M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " NAG-ASN " NAG A2001 " - " ASN A 61 " " NAG A2002 " - " ASN A 122 " " NAG A2003 " - " ASN A 165 " " NAG A2004 " - " ASN A 603 " " NAG A2005 " - " ASN A 657 " " NAG B2001 " - " ASN B 61 " " NAG B2002 " - " ASN B 122 " " NAG B2003 " - " ASN B 165 " " NAG B2004 " - " ASN B 234 " " NAG B2005 " - " ASN B 331 " " NAG B2006 " - " ASN B 603 " " NAG B2007 " - " ASN B 657 " " NAG C2001 " - " ASN C 61 " " NAG C2002 " - " ASN C 122 " " NAG C2003 " - " ASN C 165 " " NAG C2004 " - " ASN C 331 " " NAG C2005 " - " ASN C 603 " " NAG C2006 " - " ASN C 657 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 282 " " NAG F 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 343 " " NAG H 1 " - " ASN A 616 " " NAG I 1 " - " ASN A 709 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1074 " " NAG M 1 " - " ASN A1098 " " NAG N 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 282 " " NAG P 1 " - " ASN B 343 " " NAG Q 1 " - " ASN B 616 " " NAG R 1 " - " ASN B 709 " " NAG S 1 " - " ASN B 717 " " NAG T 1 " - " ASN B 801 " " NAG U 1 " - " ASN B1074 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 234 " " NAG Y 1 " - " ASN C 282 " " NAG Z 1 " - " ASN C 343 " " NAG a 1 " - " ASN C 616 " " NAG b 1 " - " ASN C 709 " " NAG c 1 " - " ASN C 717 " " NAG d 1 " - " ASN C 801 " " NAG e 1 " - " ASN C1074 " " NAG f 1 " - " ASN C1098 " " NAG g 1 " - " ASN C1134 " Time building additional restraints: 10.48 Conformation dependent library (CDL) restraints added in 4.4 seconds 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5692 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 47 sheets defined 25.1% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.89 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 removed outlier: 3.606A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.504A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 737 through 744 removed outlier: 3.885A pdb=" N TYR A 741 " --> pdb=" O ASP A 737 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ILE A 742 " --> pdb=" O CYS A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.683A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.908A pdb=" N ALA A 766 " --> pdb=" O GLN A 762 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N THR A 768 " --> pdb=" O ASN A 764 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY A 769 " --> pdb=" O ARG A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.671A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 884 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 898 through 909 removed outlier: 3.700A pdb=" N MET A 902 " --> pdb=" O PHE A 898 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 919 removed outlier: 3.623A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 941 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.561A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 removed outlier: 3.584A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU A 984 " --> pdb=" O ILE A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.629A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.593A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 389 removed outlier: 3.591A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 633 through 638 removed outlier: 3.789A pdb=" N THR B 638 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.640A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 removed outlier: 3.585A pdb=" N VAL B 826 " --> pdb=" O LEU B 822 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 884 Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.503A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 898 through 908 removed outlier: 3.844A pdb=" N TYR B 904 " --> pdb=" O MET B 900 " (cutoff:3.500A) Processing helix chain 'B' and resid 915 through 918 Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.608A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 982 removed outlier: 3.818A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.578A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.940A 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 Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.230A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE C 410 " --> pdb=" O VAL C 407 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 633 through 638 removed outlier: 3.603A pdb=" N THR C 638 " --> pdb=" O VAL C 635 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 754 removed outlier: 3.688A pdb=" N SER C 750 " --> pdb=" O SER C 746 " (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: 3.881A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.786A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 915 through 918 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.696A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 983 removed outlier: 3.558A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.565A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 3.610A pdb=" N SER A 60 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 37 removed outlier: 7.323A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL A 193 " --> pdb=" O TYR A 204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 42 through 43 removed outlier: 6.778A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ASN C 540 " --> pdb=" O GLU C 324 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.620A pdb=" N VAL A 47 " --> pdb=" O TYR A 279 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.805A pdb=" N TRP A 104 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 313 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 313 removed outlier: 4.937A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 325 through 326 Processing sheet with id=AA9, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.774A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL A 433 " --> pdb=" O LYS A 378 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB3, first strand: chain 'A' and resid 573 through 576 removed outlier: 4.217A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.354A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N TYR A 695 " --> pdb=" O CYS A 671 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N CYS A 671 " --> pdb=" O TYR A 695 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 717 through 728 removed outlier: 3.636A pdb=" N MET A1050 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB7, first strand: chain 'A' and resid 1076 through 1077 removed outlier: 3.501A pdb=" N VAL A1104 " --> pdb=" O GLN A1113 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A1113 " --> pdb=" O VAL A1104 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1083 removed outlier: 4.970A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.629A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.203A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL B 193 " --> pdb=" O TYR B 204 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.732A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.526A pdb=" N LEU B 84 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B 127 " --> pdb=" O VAL B 120 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 318 removed outlier: 5.681A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY B 593 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 323 through 328 removed outlier: 6.375A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ASN B 540 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N THR B 588 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR B 553 " --> pdb=" O ASP B 586 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 586 " --> pdb=" O THR B 553 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ALA B 575 " --> pdb=" O GLY B 566 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY B 566 " --> pdb=" O ALA B 575 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.037A pdb=" N ALA B 397 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE B 358 " --> pdb=" O VAL B 395 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC8, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.116A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.606A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 717 through 719 removed outlier: 3.510A pdb=" N GLU B 725 " --> pdb=" O PHE B1062 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 717 through 719 removed outlier: 3.720A pdb=" N GLY B1059 " --> pdb=" O ALA B1056 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.572A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1081 through 1083 removed outlier: 4.932A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.653A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.573A pdb=" N ARG C 273 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.962A pdb=" N LEU C 84 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AE1, first strand: chain 'C' and resid 191 through 197 removed outlier: 3.550A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.532A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 311 through 313 removed outlier: 3.532A pdb=" N GLY C 311 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR C 599 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.552A pdb=" N TYR C 396 " --> pdb=" O SER C 514 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N CYS C 432 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N VAL C 433 " --> pdb=" O LYS C 378 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AE6, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.316A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 712 through 728 removed outlier: 6.849A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1047 through 1050 removed outlier: 5.540A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.608A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.779A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS C1082 " --> pdb=" O VAL C1133 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2370 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.05 Time building geometry restraints manager: 11.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 7824 1.35 - 1.47: 6690 1.47 - 1.60: 10744 1.60 - 1.72: 0 1.72 - 1.85: 129 Bond restraints: 25387 Sorted by residual: bond pdb=" C1 NAG X 2 " pdb=" O5 NAG X 2 " ideal model delta sigma weight residual 1.406 1.491 -0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" C PRO C 986 " pdb=" N PRO C 987 " ideal model delta sigma weight residual 1.333 1.378 -0.044 1.44e-02 4.82e+03 9.50e+00 bond pdb=" N GLY B 639 " pdb=" CA GLY B 639 " ideal model delta sigma weight residual 1.444 1.478 -0.034 1.19e-02 7.06e+03 7.98e+00 bond pdb=" N SER B 640 " pdb=" CA SER B 640 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.11e+00 bond pdb=" C PRO B 986 " pdb=" N PRO B 987 " ideal model delta sigma weight residual 1.334 1.382 -0.048 2.34e-02 1.83e+03 4.27e+00 ... (remaining 25382 not shown) Histogram of bond angle deviations from ideal: 98.82 - 105.85: 529 105.85 - 112.89: 13948 112.89 - 119.93: 8206 119.93 - 126.97: 11637 126.97 - 134.01: 230 Bond angle restraints: 34550 Sorted by residual: angle pdb=" CA GLY B 639 " pdb=" C GLY B 639 " pdb=" O GLY B 639 " ideal model delta sigma weight residual 121.30 117.29 4.01 9.80e-01 1.04e+00 1.68e+01 angle pdb=" N CYS C 525 " pdb=" CA CYS C 525 " pdb=" C CYS C 525 " ideal model delta sigma weight residual 107.88 113.03 -5.15 1.41e+00 5.03e-01 1.33e+01 angle pdb=" N ILE A 666 " pdb=" CA ILE A 666 " pdb=" C ILE A 666 " ideal model delta sigma weight residual 111.62 108.93 2.69 7.90e-01 1.60e+00 1.16e+01 angle pdb=" N THR C 124 " pdb=" CA THR C 124 " pdb=" C THR C 124 " ideal model delta sigma weight residual 113.43 109.18 4.25 1.26e+00 6.30e-01 1.14e+01 angle pdb=" CB LYS C 195 " pdb=" CG LYS C 195 " pdb=" CD LYS C 195 " ideal model delta sigma weight residual 111.30 118.66 -7.36 2.30e+00 1.89e-01 1.02e+01 ... (remaining 34545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.53: 14971 22.53 - 45.06: 927 45.06 - 67.59: 137 67.59 - 90.12: 47 90.12 - 112.65: 25 Dihedral angle restraints: 16107 sinusoidal: 7263 harmonic: 8844 Sorted by residual: 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 93.00 178.75 -85.75 1 1.00e+01 1.00e-02 8.89e+01 dihedral pdb=" CB CYS A 662 " pdb=" SG CYS A 662 " pdb=" SG CYS A 671 " pdb=" CB CYS A 671 " ideal model delta sinusoidal sigma weight residual -86.00 -164.13 78.13 1 1.00e+01 1.00e-02 7.63e+01 dihedral pdb=" CB CYS A 738 " pdb=" SG CYS A 738 " pdb=" SG CYS A 760 " pdb=" CB CYS A 760 " ideal model delta sinusoidal sigma weight residual -86.00 -158.49 72.49 1 1.00e+01 1.00e-02 6.71e+01 ... (remaining 16104 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 3932 0.097 - 0.195: 219 0.195 - 0.292: 7 0.292 - 0.390: 2 0.390 - 0.487: 2 Chirality restraints: 4162 Sorted by residual: chirality pdb=" C1 NAG C2002 " pdb=" ND2 ASN C 122 " pdb=" C2 NAG C2002 " pdb=" O5 NAG C2002 " both_signs ideal model delta sigma weight residual False -2.40 -1.91 -0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" C1 NAG A2002 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A2002 " pdb=" O5 NAG A2002 " both_signs ideal model delta sigma weight residual False -2.40 -1.95 -0.45 2.00e-01 2.50e+01 5.09e+00 chirality pdb=" C1 NAG B2001 " pdb=" ND2 ASN B 61 " pdb=" C2 NAG B2001 " pdb=" O5 NAG B2001 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.42e+00 ... (remaining 4159 not shown) Planarity restraints: 4410 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 985 " -0.035 5.00e-02 4.00e+02 5.23e-02 4.38e+00 pdb=" N PRO A 986 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 986 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 986 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.030 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO A 987 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B1056 " -0.026 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO B1057 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B1057 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B1057 " -0.022 5.00e-02 4.00e+02 ... (remaining 4407 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 310 2.64 - 3.20: 22556 3.20 - 3.77: 35274 3.77 - 4.33: 45895 4.33 - 4.90: 77158 Nonbonded interactions: 181193 Sorted by model distance: nonbonded pdb=" OG1 THR C 393 " pdb=" OE2 GLU C 516 " model vdw 2.071 2.440 nonbonded pdb=" OG1 THR A 618 " pdb=" OE1 GLU A 619 " model vdw 2.164 2.440 nonbonded pdb=" O THR A 998 " pdb=" NE2 GLN A1002 " model vdw 2.167 2.520 nonbonded pdb=" OG1 THR A 124 " pdb=" O6 NAG A2002 " model vdw 2.169 2.440 nonbonded pdb=" OG1 THR B 393 " pdb=" OE2 GLU B 516 " model vdw 2.187 2.440 ... (remaining 181188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 27 through 621 or resid 635 through 827 or resid 855 throu \ gh 1146 or resid 2001 through 2005)) selection = (chain 'C' and (resid 27 through 621 or resid 635 through 827 or resid 855 throu \ gh 1146 or resid 2001 through 2005)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.840 Set stop_for_unknowns flag: 0.010 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: 13.050 Check model and map are aligned: 0.390 Set scattering table: 0.250 Process input model: 65.670 Find NCS groups from input model: 2.100 Set up NCS constraints: 0.410 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.005 0.085 25387 Z= 0.299 Angle : 0.657 7.798 34550 Z= 0.332 Chirality : 0.049 0.487 4162 Planarity : 0.004 0.052 4362 Dihedral : 14.905 112.654 10313 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.35 % Favored : 93.59 % Rotamer: Outliers : 0.04 % Allowed : 0.15 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.15), residues: 2993 helix: 1.44 (0.22), residues: 660 sheet: -0.65 (0.20), residues: 672 loop : -1.75 (0.14), residues: 1661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 353 HIS 0.008 0.001 HIS C1064 PHE 0.021 0.001 PHE A 906 TYR 0.017 0.001 TYR B 91 ARG 0.006 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 2657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 2.932 Fit side-chains revert: symmetry clash REVERT: B 1029 MET cc_start: 0.8976 (tmm) cc_final: 0.8678 (tmm) REVERT: C 410 ILE cc_start: 0.9235 (mm) cc_final: 0.9027 (mt) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.3170 time to fit residues: 68.0032 Evaluate side-chains 74 residues out of total 2657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 2.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 255 optimal weight: 0.0980 chunk 229 optimal weight: 9.9990 chunk 127 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 122 optimal weight: 4.9990 chunk 237 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 144 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 275 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1002 GLN ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 751 ASN B1088 HIS C 394 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.0624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 25387 Z= 0.176 Angle : 0.593 10.333 34550 Z= 0.290 Chirality : 0.046 0.454 4162 Planarity : 0.004 0.050 4362 Dihedral : 10.114 100.818 4907 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.68 % Favored : 94.25 % Rotamer: Outliers : 0.49 % Allowed : 5.34 % Favored : 94.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.15), residues: 2993 helix: 1.41 (0.21), residues: 699 sheet: -0.50 (0.20), residues: 675 loop : -1.73 (0.14), residues: 1619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 353 HIS 0.013 0.001 HIS C1064 PHE 0.018 0.001 PHE C 347 TYR 0.014 0.001 TYR B1067 ARG 0.004 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 2657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 3.216 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 740 MET cc_start: 0.7917 (mmm) cc_final: 0.7673 (mmt) REVERT: B 855 PHE cc_start: 0.7293 (m-80) cc_final: 0.6457 (m-10) REVERT: B 1029 MET cc_start: 0.9002 (tmm) cc_final: 0.8597 (tmm) REVERT: C 981 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8842 (pp) outliers start: 13 outliers final: 8 residues processed: 106 average time/residue: 0.3220 time to fit residues: 59.9348 Evaluate side-chains 91 residues out of total 2657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 2.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 1027 THR Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 990 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 152 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 229 optimal weight: 1.9990 chunk 187 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 245 optimal weight: 0.9980 chunk 273 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 221 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 25387 Z= 0.244 Angle : 0.598 10.172 34550 Z= 0.294 Chirality : 0.046 0.451 4162 Planarity : 0.004 0.048 4362 Dihedral : 8.811 96.052 4907 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.78 % Favored : 93.15 % Rotamer: Outliers : 0.64 % Allowed : 9.33 % Favored : 90.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.15), residues: 2993 helix: 1.39 (0.21), residues: 699 sheet: -0.55 (0.20), residues: 687 loop : -1.72 (0.15), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 353 HIS 0.004 0.001 HIS A1048 PHE 0.040 0.001 PHE C 456 TYR 0.020 0.001 TYR A 91 ARG 0.007 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 2.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 1029 MET cc_start: 0.9010 (tmm) cc_final: 0.8542 (tmm) REVERT: C 981 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8855 (pp) outliers start: 17 outliers final: 9 residues processed: 103 average time/residue: 0.3134 time to fit residues: 57.5248 Evaluate side-chains 91 residues out of total 2657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 2.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 990 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 272 optimal weight: 4.9990 chunk 207 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 131 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 276 optimal weight: 1.9990 chunk 292 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 262 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.1065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 25387 Z= 0.285 Angle : 0.613 9.633 34550 Z= 0.304 Chirality : 0.046 0.438 4162 Planarity : 0.004 0.048 4362 Dihedral : 8.173 85.977 4907 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.68 % Favored : 93.25 % Rotamer: Outliers : 0.98 % Allowed : 13.06 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.15), residues: 2993 helix: 1.26 (0.21), residues: 693 sheet: -0.56 (0.20), residues: 676 loop : -1.76 (0.15), residues: 1624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 353 HIS 0.004 0.001 HIS A1048 PHE 0.019 0.002 PHE C1121 TYR 0.021 0.001 TYR A 91 ARG 0.007 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 2657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 88 time to evaluate : 2.724 Fit side-chains revert: symmetry clash REVERT: B 490 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.6994 (t80) REVERT: B 1029 MET cc_start: 0.9028 (tmm) cc_final: 0.8522 (tmm) REVERT: C 981 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8864 (pp) outliers start: 26 outliers final: 16 residues processed: 109 average time/residue: 0.3098 time to fit residues: 59.6095 Evaluate side-chains 94 residues out of total 2657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 76 time to evaluate : 2.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 243 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 4 optimal weight: 0.0050 chunk 218 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 249 optimal weight: 1.9990 chunk 202 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 149 optimal weight: 0.8980 chunk 262 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1005 GLN ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25387 Z= 0.169 Angle : 0.562 9.606 34550 Z= 0.276 Chirality : 0.045 0.438 4162 Planarity : 0.003 0.047 4362 Dihedral : 7.765 82.917 4907 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.65 % Favored : 94.29 % Rotamer: Outliers : 1.02 % Allowed : 14.38 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.15), residues: 2993 helix: 1.42 (0.21), residues: 693 sheet: -0.49 (0.20), residues: 690 loop : -1.68 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 104 HIS 0.003 0.001 HIS B1064 PHE 0.021 0.001 PHE A 201 TYR 0.014 0.001 TYR A1067 ARG 0.006 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 2657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 89 time to evaluate : 2.692 Fit side-chains revert: symmetry clash REVERT: B 490 PHE cc_start: 0.7520 (OUTLIER) cc_final: 0.7050 (t80) REVERT: B 540 ASN cc_start: 0.7839 (OUTLIER) cc_final: 0.7334 (p0) REVERT: B 697 MET cc_start: 0.7487 (ttm) cc_final: 0.7262 (ttp) REVERT: B 740 MET cc_start: 0.7926 (mmt) cc_final: 0.7685 (mmm) REVERT: B 1029 MET cc_start: 0.9061 (tmm) cc_final: 0.8588 (tmm) outliers start: 27 outliers final: 16 residues processed: 110 average time/residue: 0.3194 time to fit residues: 62.7789 Evaluate side-chains 97 residues out of total 2657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 2.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 98 optimal weight: 1.9990 chunk 263 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 171 optimal weight: 0.9990 chunk 72 optimal weight: 0.0670 chunk 293 optimal weight: 2.9990 chunk 243 optimal weight: 0.6980 chunk 135 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 overall best weight: 1.1524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** B 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 25387 Z= 0.195 Angle : 0.567 9.622 34550 Z= 0.277 Chirality : 0.045 0.430 4162 Planarity : 0.003 0.048 4362 Dihedral : 7.509 78.957 4907 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.05 % Favored : 93.89 % Rotamer: Outliers : 1.35 % Allowed : 15.66 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.15), residues: 2993 helix: 1.42 (0.21), residues: 692 sheet: -0.46 (0.20), residues: 685 loop : -1.66 (0.15), residues: 1616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 104 HIS 0.002 0.001 HIS C 49 PHE 0.021 0.001 PHE C 456 TYR 0.015 0.001 TYR A1067 ARG 0.006 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 86 time to evaluate : 2.569 Fit side-chains revert: symmetry clash REVERT: B 490 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.7069 (t80) REVERT: B 540 ASN cc_start: 0.7809 (OUTLIER) cc_final: 0.7279 (p0) REVERT: B 697 MET cc_start: 0.7442 (ttm) cc_final: 0.7219 (ttp) REVERT: B 740 MET cc_start: 0.7960 (mmt) cc_final: 0.7749 (mmm) REVERT: B 1029 MET cc_start: 0.9060 (tmm) cc_final: 0.8550 (tmm) outliers start: 36 outliers final: 22 residues processed: 118 average time/residue: 0.2823 time to fit residues: 59.7425 Evaluate side-chains 105 residues out of total 2657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 81 time to evaluate : 2.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 867 ASP Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 282 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 167 optimal weight: 5.9990 chunk 214 optimal weight: 6.9990 chunk 165 optimal weight: 0.7980 chunk 246 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 chunk 182 optimal weight: 2.9990 chunk 178 optimal weight: 0.5980 chunk 134 optimal weight: 0.4980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS C 354 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 25387 Z= 0.165 Angle : 0.553 9.608 34550 Z= 0.270 Chirality : 0.045 0.425 4162 Planarity : 0.003 0.050 4362 Dihedral : 7.246 74.451 4907 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.51 % Favored : 94.42 % Rotamer: Outliers : 1.39 % Allowed : 16.26 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.16), residues: 2993 helix: 1.48 (0.21), residues: 690 sheet: -0.43 (0.20), residues: 693 loop : -1.62 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 104 HIS 0.002 0.000 HIS B1064 PHE 0.024 0.001 PHE C 456 TYR 0.015 0.001 TYR A1067 ARG 0.007 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 2657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 92 time to evaluate : 2.905 Fit side-chains revert: symmetry clash REVERT: A 1029 MET cc_start: 0.8835 (tpp) cc_final: 0.8511 (tmm) REVERT: B 490 PHE cc_start: 0.7389 (OUTLIER) cc_final: 0.6963 (t80) REVERT: B 540 ASN cc_start: 0.7794 (OUTLIER) cc_final: 0.7247 (p0) REVERT: B 697 MET cc_start: 0.7474 (ttm) cc_final: 0.7255 (ttp) REVERT: B 740 MET cc_start: 0.7924 (mmt) cc_final: 0.7717 (mmm) REVERT: B 1029 MET cc_start: 0.9074 (tmm) cc_final: 0.8560 (tmm) REVERT: C 981 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8846 (pp) outliers start: 37 outliers final: 25 residues processed: 122 average time/residue: 0.3001 time to fit residues: 65.2651 Evaluate side-chains 112 residues out of total 2657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 84 time to evaluate : 2.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 180 optimal weight: 1.9990 chunk 116 optimal weight: 5.9990 chunk 174 optimal weight: 0.9980 chunk 87 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 56 optimal weight: 6.9990 chunk 185 optimal weight: 7.9990 chunk 198 optimal weight: 0.9990 chunk 144 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 229 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 25387 Z= 0.157 Angle : 0.559 12.227 34550 Z= 0.271 Chirality : 0.045 0.419 4162 Planarity : 0.003 0.048 4362 Dihedral : 7.017 68.849 4907 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.58 % Favored : 94.35 % Rotamer: Outliers : 1.66 % Allowed : 16.41 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.16), residues: 2993 helix: 1.55 (0.21), residues: 685 sheet: -0.39 (0.20), residues: 695 loop : -1.59 (0.15), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 104 HIS 0.002 0.000 HIS B1064 PHE 0.028 0.001 PHE C 135 TYR 0.015 0.001 TYR A1067 ARG 0.006 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 89 time to evaluate : 3.002 Fit side-chains revert: symmetry clash REVERT: A 1029 MET cc_start: 0.8830 (tpp) cc_final: 0.8484 (tmm) REVERT: B 490 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6994 (t80) REVERT: B 540 ASN cc_start: 0.7792 (OUTLIER) cc_final: 0.7222 (p0) REVERT: B 697 MET cc_start: 0.7507 (ttm) cc_final: 0.7280 (ttp) REVERT: B 1029 MET cc_start: 0.9076 (tmm) cc_final: 0.8648 (tmm) REVERT: C 216 LEU cc_start: 0.5367 (OUTLIER) cc_final: 0.5144 (mm) REVERT: C 238 PHE cc_start: 0.7852 (p90) cc_final: 0.7628 (p90) REVERT: C 981 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8844 (pp) REVERT: C 1031 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7459 (tm-30) outliers start: 44 outliers final: 30 residues processed: 129 average time/residue: 0.2810 time to fit residues: 65.6536 Evaluate side-chains 118 residues out of total 2657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 84 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 981 LEU Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 265 optimal weight: 1.9990 chunk 279 optimal weight: 0.9980 chunk 255 optimal weight: 6.9990 chunk 272 optimal weight: 0.9980 chunk 163 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 245 optimal weight: 9.9990 chunk 257 optimal weight: 0.9980 chunk 271 optimal weight: 0.7980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 25387 Z= 0.174 Angle : 0.572 14.058 34550 Z= 0.276 Chirality : 0.045 0.415 4162 Planarity : 0.003 0.047 4362 Dihedral : 6.885 64.736 4907 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.55 % Favored : 94.39 % Rotamer: Outliers : 1.47 % Allowed : 16.82 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2993 helix: 1.54 (0.21), residues: 684 sheet: -0.33 (0.20), residues: 677 loop : -1.57 (0.15), residues: 1632 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 104 HIS 0.003 0.000 HIS B1064 PHE 0.027 0.001 PHE C 456 TYR 0.015 0.001 TYR A1067 ARG 0.006 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 85 time to evaluate : 2.806 Fit side-chains revert: symmetry clash REVERT: A 1029 MET cc_start: 0.8835 (tpp) cc_final: 0.8482 (tmm) REVERT: B 490 PHE cc_start: 0.7459 (OUTLIER) cc_final: 0.7030 (t80) REVERT: B 540 ASN cc_start: 0.7800 (OUTLIER) cc_final: 0.7235 (p0) REVERT: B 697 MET cc_start: 0.7493 (ttm) cc_final: 0.7283 (ttp) REVERT: B 740 MET cc_start: 0.8062 (mmm) cc_final: 0.7846 (mmt) REVERT: B 1029 MET cc_start: 0.9083 (tmm) cc_final: 0.8649 (tmm) REVERT: C 216 LEU cc_start: 0.5398 (OUTLIER) cc_final: 0.5172 (mm) REVERT: C 238 PHE cc_start: 0.7854 (p90) cc_final: 0.7639 (p90) outliers start: 39 outliers final: 34 residues processed: 120 average time/residue: 0.2861 time to fit residues: 61.5678 Evaluate side-chains 121 residues out of total 2657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 84 time to evaluate : 2.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 178 optimal weight: 0.9990 chunk 287 optimal weight: 0.9990 chunk 175 optimal weight: 0.8980 chunk 136 optimal weight: 9.9990 chunk 200 optimal weight: 4.9990 chunk 301 optimal weight: 0.3980 chunk 277 optimal weight: 0.8980 chunk 240 optimal weight: 0.5980 chunk 24 optimal weight: 5.9990 chunk 185 optimal weight: 3.9990 chunk 147 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 25387 Z= 0.159 Angle : 0.571 13.095 34550 Z= 0.275 Chirality : 0.045 0.411 4162 Planarity : 0.003 0.047 4362 Dihedral : 6.734 59.468 4907 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.45 % Favored : 94.49 % Rotamer: Outliers : 1.51 % Allowed : 17.01 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.16), residues: 2993 helix: 1.49 (0.21), residues: 691 sheet: -0.30 (0.20), residues: 687 loop : -1.58 (0.15), residues: 1615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 104 HIS 0.003 0.000 HIS B1064 PHE 0.020 0.001 PHE C 347 TYR 0.015 0.001 TYR A1067 ARG 0.007 0.000 ARG B 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5986 Ramachandran restraints generated. 2993 Oldfield, 0 Emsley, 2993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 2657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 87 time to evaluate : 3.040 Fit side-chains revert: symmetry clash REVERT: A 1029 MET cc_start: 0.8809 (tpp) cc_final: 0.8458 (tmm) REVERT: B 490 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.7137 (t80) REVERT: B 540 ASN cc_start: 0.7796 (OUTLIER) cc_final: 0.7225 (p0) REVERT: B 697 MET cc_start: 0.7529 (ttm) cc_final: 0.7325 (ttp) REVERT: B 1029 MET cc_start: 0.9078 (tmm) cc_final: 0.8659 (tmm) REVERT: C 216 LEU cc_start: 0.5403 (OUTLIER) cc_final: 0.5175 (mm) REVERT: C 238 PHE cc_start: 0.7827 (p90) cc_final: 0.7617 (p90) outliers start: 40 outliers final: 35 residues processed: 121 average time/residue: 0.2827 time to fit residues: 61.8417 Evaluate side-chains 121 residues out of total 2657 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 83 time to evaluate : 2.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 595 VAL Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 738 CYS Chi-restraints excluded: chain A residue 856 ASN Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 160 TYR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 432 CYS Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 490 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 540 ASN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 632 THR Chi-restraints excluded: chain B residue 931 ILE Chi-restraints excluded: chain B residue 950 ASP Chi-restraints excluded: chain B residue 981 LEU Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 137 ASN Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 389 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 725 GLU Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 887 THR Chi-restraints excluded: chain C residue 950 ASP Chi-restraints excluded: chain C residue 990 GLU Chi-restraints excluded: chain C residue 1133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 303 random chunks: chunk 190 optimal weight: 0.8980 chunk 256 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 221 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 chunk 240 optimal weight: 2.9990 chunk 100 optimal weight: 0.0470 chunk 247 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 777 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN C 777 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.103093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.066649 restraints weight = 68688.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.069389 restraints weight = 38651.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.071193 restraints weight = 27593.160| |-----------------------------------------------------------------------------| r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 25387 Z= 0.147 Angle : 0.559 12.969 34550 Z= 0.269 Chirality : 0.045 0.410 4162 Planarity : 0.004 0.070 4362 Dihedral : 6.531 58.775 4907 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.05 % Favored : 94.89 % Rotamer: Outliers : 1.43 % Allowed : 17.20 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.16), residues: 2993 helix: 1.53 (0.21), residues: 691 sheet: -0.25 (0.20), residues: 692 loop : -1.54 (0.15), residues: 1610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 104 HIS 0.003 0.000 HIS B1064 PHE 0.029 0.001 PHE C 456 TYR 0.015 0.001 TYR A1067 ARG 0.006 0.000 ARG B 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3624.40 seconds wall clock time: 67 minutes 49.79 seconds (4069.79 seconds total)