Starting phenix.real_space_refine on Fri Aug 9 09:17:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fce_31525/08_2024/7fce_31525.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fce_31525/08_2024/7fce_31525.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fce_31525/08_2024/7fce_31525.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fce_31525/08_2024/7fce_31525.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fce_31525/08_2024/7fce_31525.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7fce_31525/08_2024/7fce_31525.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 114 5.16 5 C 16239 2.51 5 N 4157 2.21 5 O 5032 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 25542 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8158 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1043, 8142 Classifications: {'peptide': 1043} Link IDs: {'PTRANS': 51, 'TRANS': 991} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1043, 8142 Classifications: {'peptide': 1043} Link IDs: {'PTRANS': 51, 'TRANS': 991} Chain breaks: 8 bond proxies already assigned to first conformer: 8305 Chain: "B" Number of atoms: 8146 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 51, 'TRANS': 989} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 51, 'TRANS': 989} Chain breaks: 8 bond proxies already assigned to first conformer: 8293 Chain: "C" Number of atoms: 8146 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 51, 'TRANS': 989} Chain breaks: 8 Conformer: "B" Number of residues, atoms: 1041, 8130 Classifications: {'peptide': 1041} Link IDs: {'PTRANS': 51, 'TRANS': 989} Chain breaks: 8 bond proxies already assigned to first conformer: 8293 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: "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: "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: "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: "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: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Time building chain proxies: 25.84, per 1000 atoms: 1.01 Number of scatterers: 25542 At special positions: 0 Unit cell: (135.042, 136.14, 162.489, 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 114 16.00 O 5032 8.00 N 4157 7.00 C 16239 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=45, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.02 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.04 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.04 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.04 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.04 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.06 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.02 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.04 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.04 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.04 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.04 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.04 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 15 " - pdb=" SG CYS C 136 " distance=2.05 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 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=2.05 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.02 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.04 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.04 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.04 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.05 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 E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 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 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 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 A1301 " - " ASN A 282 " " NAG A1302 " - " ASN A 331 " " NAG A1303 " - " ASN A 343 " " NAG A1304 " - " ASN A 657 " " NAG A1305 " - " ASN A 709 " " NAG A1306 " - " ASN A1074 " " NAG A1307 " - " ASN A 370 " " NAG A1308 " - " ASN A 616 " " NAG B1301 " - " ASN B 282 " " NAG B1302 " - " ASN B 331 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 657 " " NAG B1305 " - " ASN B 709 " " NAG B1306 " - " ASN B1074 " " NAG B1307 " - " ASN B 370 " " NAG B1308 " - " ASN B 61 " " NAG C1301 " - " ASN C 282 " " NAG C1302 " - " ASN C 331 " " NAG C1303 " - " ASN C 343 " " NAG C1304 " - " ASN C 657 " " NAG C1305 " - " ASN C 709 " " NAG C1306 " - " ASN C1074 " " NAG C1307 " - " ASN C 370 " " NAG C1308 " - " ASN C 61 " " NAG D 1 " - " ASN A 61 " " NAG E 1 " - " ASN A 17 " " NAG F 1 " - " ASN A 122 " " NAG G 1 " - " ASN A 165 " " NAG H 1 " - " ASN A 234 " " NAG J 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG L 1 " - " ASN A1098 " " NAG M 1 " - " ASN A1134 " " NAG O 1 " - " ASN B 17 " " NAG P 1 " - " ASN B 122 " " NAG Q 1 " - " ASN B 165 " " NAG R 1 " - " ASN B 234 " " NAG S 1 " - " ASN B 616 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG Y 1 " - " ASN C 17 " " NAG Z 1 " - " ASN C 122 " " NAG a 1 " - " ASN C 165 " " NAG b 1 " - " ASN C 234 " " NAG c 1 " - " ASN C 616 " " NAG d 1 " - " ASN C 717 " " NAG e 1 " - " ASN C 801 " " NAG f 1 " - " ASN C1098 " " NAG g 1 " - " ASN C1134 " Time building additional restraints: 9.83 Conformation dependent library (CDL) restraints added in 8.7 seconds 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5864 Finding SS restraints... Secondary structure from input PDB file: 69 helices and 42 sheets defined 25.6% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.23 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.704A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.191A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 756 through 783 removed outlier: 3.752A pdb=" N CYS A 760 " --> pdb=" O TYR A 756 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 836 through 840 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.137A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.210A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (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 982 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.438A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 369 removed outlier: 3.653A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.190A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 756 through 783 removed outlier: 3.751A pdb=" N CYS B 760 " --> pdb=" O TYR B 756 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 836 through 840 Processing helix chain 'B' and resid 848 through 855 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 890 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.137A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.209A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (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 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.438A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1146 Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 366 through 372 removed outlier: 4.094A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.671A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.191A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 756 through 783 removed outlier: 3.750A pdb=" N CYS C 760 " --> pdb=" O TYR C 756 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 836 through 840 Processing helix chain 'C' and resid 848 through 855 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 890 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.137A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.210A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (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 982 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.438A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1141 through 1146 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 4.205A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.030A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.877A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 133 through 135 removed outlier: 6.136A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 328 removed outlier: 6.418A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN A 542 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.334A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.322A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.629A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.070A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.405A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AB6, first strand: chain 'B' and resid 27 through 30 removed outlier: 4.204A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.961A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.031A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.876A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 133 through 135 removed outlier: 6.645A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AC2, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.418A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.334A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.321A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 712 through 715 removed outlier: 3.629A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N GLN B1106 " --> pdb=" O GLU B1111 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU B1111 " --> pdb=" O GLN B1106 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 718 through 728 removed outlier: 6.070A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.406A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AD2, first strand: chain 'C' and resid 27 through 30 removed outlier: 4.204A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.030A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 83 through 85 removed outlier: 3.876A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.644A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 311 through 314 Processing sheet with id=AD7, first strand: chain 'C' and resid 324 through 328 removed outlier: 6.417A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.400A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY C 566 " --> pdb=" O ASP C 574 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.333A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.321A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 712 through 715 removed outlier: 3.629A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN C1106 " --> pdb=" O GLU C1111 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU C1111 " --> pdb=" O GLN C1106 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 718 through 728 removed outlier: 6.071A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.406A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 1037 hydrogen bonds defined for protein. 2796 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: 10.77 Time building geometry restraints manager: 10.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7816 1.34 - 1.47: 6740 1.47 - 1.59: 11403 1.59 - 1.72: 0 1.72 - 1.85: 138 Bond restraints: 26097 Sorted by residual: bond pdb=" C ASP A 138 " pdb=" N PRO A 139 " ideal model delta sigma weight residual 1.329 1.372 -0.043 1.25e-02 6.40e+03 1.16e+01 bond pdb=" C LYS A 462 " pdb=" N PRO A 463 " ideal model delta sigma weight residual 1.332 1.373 -0.041 1.30e-02 5.92e+03 1.01e+01 bond pdb=" N ARG B 457 " pdb=" CA ARG B 457 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.21e-02 6.83e+03 8.84e+00 bond pdb=" N SER A 494 " pdb=" CA SER A 494 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.18e-02 7.18e+03 8.52e+00 bond pdb=" N ILE A 472 " pdb=" CA ILE A 472 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.09e+00 ... (remaining 26092 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.62: 682 106.62 - 113.52: 14535 113.52 - 120.43: 9817 120.43 - 127.33: 10266 127.33 - 134.24: 215 Bond angle restraints: 35515 Sorted by residual: angle pdb=" N CYS A 525 " pdb=" CA CYS A 525 " pdb=" C CYS A 525 " ideal model delta sigma weight residual 110.80 119.21 -8.41 2.13e+00 2.20e-01 1.56e+01 angle pdb=" N CYS C 525 " pdb=" CA CYS C 525 " pdb=" C CYS C 525 " ideal model delta sigma weight residual 110.80 119.21 -8.41 2.13e+00 2.20e-01 1.56e+01 angle pdb=" N CYS B 525 " pdb=" CA CYS B 525 " pdb=" C CYS B 525 " ideal model delta sigma weight residual 110.80 119.17 -8.37 2.13e+00 2.20e-01 1.55e+01 angle pdb=" N LEU A 455 " pdb=" CA LEU A 455 " pdb=" C LEU A 455 " ideal model delta sigma weight residual 113.50 108.67 4.83 1.23e+00 6.61e-01 1.54e+01 angle pdb=" C TYR A 495 " pdb=" CA TYR A 495 " pdb=" CB TYR A 495 " ideal model delta sigma weight residual 109.75 103.39 6.36 1.65e+00 3.67e-01 1.49e+01 ... (remaining 35510 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 15381 17.58 - 35.16: 896 35.16 - 52.74: 178 52.74 - 70.32: 95 70.32 - 87.90: 28 Dihedral angle restraints: 16578 sinusoidal: 7466 harmonic: 9112 Sorted by residual: dihedral pdb=" CA LEU B 368 " pdb=" C LEU B 368 " pdb=" N TYR B 369 " pdb=" CA TYR B 369 " ideal model delta harmonic sigma weight residual -180.00 -156.33 -23.67 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA SER C 371 " pdb=" C SER C 371 " pdb=" N THR C 372 " pdb=" CA THR C 372 " ideal model delta harmonic sigma weight residual -180.00 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA SER A 371 " pdb=" C SER A 371 " pdb=" N THR A 372 " pdb=" CA THR A 372 " ideal model delta harmonic sigma weight residual -180.00 -156.96 -23.04 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 16575 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3265 0.079 - 0.159: 955 0.159 - 0.238: 46 0.238 - 0.318: 2 0.318 - 0.397: 2 Chirality restraints: 4270 Sorted by residual: chirality pdb=" C1 NAG B1307 " pdb=" ND2 ASN B 370 " pdb=" C2 NAG B1307 " pdb=" O5 NAG B1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.00 -0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CA TYR A 495 " pdb=" N TYR A 495 " pdb=" C TYR A 495 " pdb=" CB TYR A 495 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.72e+00 chirality pdb=" C1 NAG C1307 " pdb=" ND2 ASN C 370 " pdb=" C2 NAG C1307 " pdb=" O5 NAG C1307 " both_signs ideal model delta sigma weight residual False -2.40 -2.11 -0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 4267 not shown) Planarity restraints: 4542 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B1307 " 0.333 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG B1307 " -0.077 2.00e-02 2.50e+03 pdb=" C8 NAG B1307 " 0.042 2.00e-02 2.50e+03 pdb=" N2 NAG B1307 " -0.504 2.00e-02 2.50e+03 pdb=" O7 NAG B1307 " 0.205 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A1307 " 0.330 2.00e-02 2.50e+03 2.82e-01 9.91e+02 pdb=" C7 NAG A1307 " -0.084 2.00e-02 2.50e+03 pdb=" C8 NAG A1307 " 0.177 2.00e-02 2.50e+03 pdb=" N2 NAG A1307 " -0.494 2.00e-02 2.50e+03 pdb=" O7 NAG A1307 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C1307 " 0.135 2.00e-02 2.50e+03 1.11e-01 1.53e+02 pdb=" C7 NAG C1307 " -0.037 2.00e-02 2.50e+03 pdb=" C8 NAG C1307 " 0.101 2.00e-02 2.50e+03 pdb=" N2 NAG C1307 " -0.175 2.00e-02 2.50e+03 pdb=" O7 NAG C1307 " -0.023 2.00e-02 2.50e+03 ... (remaining 4539 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 8440 2.85 - 3.37: 20721 3.37 - 3.88: 40988 3.88 - 4.39: 47432 4.39 - 4.90: 82022 Nonbonded interactions: 199603 Sorted by model distance: nonbonded pdb=" OD1 ASN A 777 " pdb=" NH1BARG A1019 " model vdw 2.343 3.120 nonbonded pdb=" OD1 ASN C 777 " pdb=" NH1BARG C1019 " model vdw 2.344 3.120 nonbonded pdb=" OD1 ASN B 777 " pdb=" NH1BARG B1019 " model vdw 2.345 3.120 nonbonded pdb=" O SER B 477 " pdb=" OG1 THR B 478 " model vdw 2.346 3.040 nonbonded pdb=" O SER A 477 " pdb=" OG1 THR A 478 " model vdw 2.347 3.040 ... (remaining 199598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 70 or resid 81 through 245 or resid 262 through \ 822 or resid 824 through 1018 or resid 1020 through 1146 or resid 1301 through \ 1308)) selection = (chain 'B' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1146 or resid 1301 through 1308)) selection = (chain 'C' and (resid 14 through 822 or resid 824 through 1018 or resid 1020 thr \ ough 1146 or resid 1301 through 1308)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' 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 '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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.970 Check model and map are aligned: 0.180 Set scattering table: 0.230 Process input model: 87.020 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.240 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:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 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 : 0.010 0.081 26097 Z= 0.660 Angle : 0.978 11.739 35515 Z= 0.543 Chirality : 0.065 0.397 4270 Planarity : 0.008 0.288 4491 Dihedral : 12.930 87.899 10579 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 1.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.56 % Favored : 95.28 % Rotamer: Outliers : 0.99 % Allowed : 3.47 % Favored : 95.54 % 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: -0.85 (0.14), residues: 3077 helix: 0.89 (0.20), residues: 711 sheet: 0.63 (0.20), residues: 664 loop : -1.79 (0.13), residues: 1702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.004 TRP B 886 HIS 0.008 0.002 HIS B 49 PHE 0.022 0.004 PHE A 592 TYR 0.024 0.004 TYR C 265 ARG 0.008 0.001 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 577 time to evaluate : 2.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 904 TYR cc_start: 0.6157 (m-10) cc_final: 0.5530 (m-10) REVERT: B 844 ILE cc_start: 0.6885 (mt) cc_final: 0.6507 (mt) REVERT: C 14 GLN cc_start: 0.5295 (OUTLIER) cc_final: 0.4347 (mm-40) REVERT: C 751 ASN cc_start: 0.7140 (m110) cc_final: 0.6936 (m-40) REVERT: C 912 THR cc_start: 0.6991 (p) cc_final: 0.6786 (p) outliers start: 27 outliers final: 2 residues processed: 598 average time/residue: 0.3551 time to fit residues: 333.8807 Evaluate side-chains 293 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 290 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 331 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 5.9990 chunk 236 optimal weight: 0.9980 chunk 131 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 159 optimal weight: 5.9990 chunk 126 optimal weight: 0.8980 chunk 244 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 148 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 283 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 207 HIS A 218 GLN ** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 440 ASN A 501 ASN A 563 GLN A 580 GLN A 641 ASN A 703 ASN A 836 GLN A 919 ASN A1023 ASN A1036 GLN A1064 HIS A1083 HIS A1101 HIS B 87 ASN B 115 GLN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 GLN B 239 GLN B 245 HIS B 394 ASN B 540 ASN B 563 GLN B 580 GLN B 641 ASN B 658 ASN B 751 ASN B 925 ASN B 935 GLN B1023 ASN B1036 GLN B1054 GLN B1064 HIS C 66 HIS ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 164 ASN C 188 ASN C 218 GLN C 271 GLN C 394 ASN C 540 ASN C 563 GLN C 580 GLN C 607 GLN C 658 ASN C 703 ASN C 751 ASN C 925 ASN C1023 ASN C1036 GLN C1064 HIS Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 26097 Z= 0.243 Angle : 0.692 16.887 35515 Z= 0.351 Chirality : 0.050 0.460 4270 Planarity : 0.005 0.064 4491 Dihedral : 7.376 59.696 5001 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.65 % Favored : 96.19 % Rotamer: Outliers : 1.32 % Allowed : 9.00 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.65 % 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: -0.64 (0.14), residues: 3077 helix: 1.11 (0.20), residues: 723 sheet: 0.67 (0.20), residues: 649 loop : -1.64 (0.13), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 353 HIS 0.004 0.001 HIS A1088 PHE 0.043 0.002 PHE C 59 TYR 0.018 0.002 TYR C 756 ARG 0.008 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 340 time to evaluate : 3.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 776 LYS cc_start: 0.8483 (tttt) cc_final: 0.8171 (ttpp) REVERT: A 904 TYR cc_start: 0.6655 (m-10) cc_final: 0.6183 (m-10) REVERT: B 233 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8243 (pp) REVERT: B 472 ILE cc_start: 0.8330 (mm) cc_final: 0.8122 (mm) REVERT: B 844 ILE cc_start: 0.6739 (mt) cc_final: 0.6458 (mt) REVERT: B 936 ASP cc_start: 0.6812 (OUTLIER) cc_final: 0.6519 (m-30) REVERT: C 14 GLN cc_start: 0.4935 (OUTLIER) cc_final: 0.3894 (mm-40) outliers start: 36 outliers final: 22 residues processed: 362 average time/residue: 0.3668 time to fit residues: 210.3753 Evaluate side-chains 289 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 264 time to evaluate : 3.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 301 CYS Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 936 ASP Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 301 CYS Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 500 THR Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 940 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 235 optimal weight: 0.9990 chunk 192 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 283 optimal weight: 3.9990 chunk 306 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 chunk 281 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 HIS A 422 ASN A 751 ASN A 901 GLN A1005 GLN A1011 GLN A1054 GLN A1101 HIS B 137 ASN ** B 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 ASN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 804 GLN C 901 GLN C1054 GLN C1083 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 26097 Z= 0.371 Angle : 0.724 14.506 35515 Z= 0.377 Chirality : 0.050 0.387 4270 Planarity : 0.005 0.045 4491 Dihedral : 7.057 59.415 4997 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.20 % Favored : 95.67 % Rotamer: Outliers : 1.83 % Allowed : 9.95 % Favored : 88.22 % 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: -0.58 (0.14), residues: 3077 helix: 1.22 (0.20), residues: 698 sheet: 0.57 (0.20), residues: 627 loop : -1.49 (0.13), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C1102 HIS 0.008 0.002 HIS A1088 PHE 0.028 0.002 PHE C 168 TYR 0.029 0.002 TYR C 756 ARG 0.011 0.001 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 256 time to evaluate : 2.667 Fit side-chains revert: symmetry clash REVERT: A 326 ILE cc_start: 0.8239 (pt) cc_final: 0.8030 (pt) REVERT: A 449 TYR cc_start: 0.8468 (m-80) cc_final: 0.8250 (m-80) REVERT: A 470 THR cc_start: 0.8698 (p) cc_final: 0.8460 (p) REVERT: A 675 GLN cc_start: 0.6401 (pp30) cc_final: 0.6008 (pp30) REVERT: A 703 ASN cc_start: 0.7469 (OUTLIER) cc_final: 0.7175 (p0) REVERT: A 824 ASN cc_start: 0.8318 (m-40) cc_final: 0.8094 (m-40) REVERT: B 503 VAL cc_start: 0.9264 (p) cc_final: 0.9055 (t) REVERT: B 844 ILE cc_start: 0.6811 (mt) cc_final: 0.6538 (mt) REVERT: C 787 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8050 (mm-40) REVERT: C 804 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7202 (tt0) REVERT: C 1072 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: C 1141 LEU cc_start: 0.6854 (mp) cc_final: 0.6587 (tp) outliers start: 50 outliers final: 31 residues processed: 292 average time/residue: 0.3770 time to fit residues: 173.4562 Evaluate side-chains 231 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 197 time to evaluate : 3.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 703 ASN Chi-restraints excluded: chain A residue 827 THR Chi-restraints excluded: chain A residue 940 SER Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 724 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 703 ASN Chi-restraints excluded: chain C residue 719 THR Chi-restraints excluded: chain C residue 804 GLN Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1097 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 2.9990 chunk 213 optimal weight: 10.0000 chunk 147 optimal weight: 0.0870 chunk 31 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 chunk 190 optimal weight: 0.9990 chunk 284 optimal weight: 0.5980 chunk 301 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 269 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 ASN A 540 ASN A 935 GLN B 66 HIS B 137 ASN B 164 ASN B 207 HIS ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 ASN C 271 GLN C 641 ASN C 901 GLN C 935 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.5894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 26097 Z= 0.162 Angle : 0.555 16.372 35515 Z= 0.287 Chirality : 0.045 0.382 4270 Planarity : 0.004 0.049 4491 Dihedral : 6.592 59.699 4994 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.80 % Favored : 97.17 % Rotamer: Outliers : 1.02 % Allowed : 11.19 % Favored : 87.78 % 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: -0.26 (0.15), residues: 3077 helix: 1.60 (0.20), residues: 692 sheet: 0.75 (0.20), residues: 616 loop : -1.32 (0.14), residues: 1769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 104 HIS 0.007 0.001 HIS B 207 PHE 0.017 0.001 PHE A 329 TYR 0.017 0.001 TYR C1067 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 216 time to evaluate : 2.976 Fit side-chains revert: symmetry clash REVERT: A 449 TYR cc_start: 0.8484 (m-80) cc_final: 0.8271 (m-80) REVERT: A 470 THR cc_start: 0.8626 (p) cc_final: 0.8394 (p) REVERT: A 824 ASN cc_start: 0.8324 (m-40) cc_final: 0.8100 (m-40) REVERT: B 844 ILE cc_start: 0.6782 (mt) cc_final: 0.6536 (mt) REVERT: C 690 GLN cc_start: 0.6426 (mm110) cc_final: 0.5882 (mm-40) REVERT: C 787 GLN cc_start: 0.8522 (mm-40) cc_final: 0.8016 (mm-40) REVERT: C 1141 LEU cc_start: 0.6843 (mp) cc_final: 0.6557 (tp) outliers start: 28 outliers final: 16 residues processed: 238 average time/residue: 0.3620 time to fit residues: 140.1652 Evaluate side-chains 201 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 185 time to evaluate : 2.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 902 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 1.9990 chunk 171 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 124 optimal weight: 0.8980 chunk 257 optimal weight: 2.9990 chunk 208 optimal weight: 20.0000 chunk 0 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 270 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 394 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.6222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 26097 Z= 0.206 Angle : 0.556 16.012 35515 Z= 0.286 Chirality : 0.045 0.342 4270 Planarity : 0.004 0.041 4491 Dihedral : 6.413 58.897 4994 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.74 % Favored : 96.22 % Rotamer: Outliers : 1.21 % Allowed : 11.59 % Favored : 87.20 % 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: -0.19 (0.15), residues: 3077 helix: 1.70 (0.20), residues: 698 sheet: 0.66 (0.20), residues: 626 loop : -1.25 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.003 0.001 HIS B 49 PHE 0.017 0.001 PHE C 643 TYR 0.018 0.001 TYR C 756 ARG 0.003 0.000 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 186 time to evaluate : 2.682 Fit side-chains revert: symmetry clash REVERT: A 100 ILE cc_start: 0.7942 (mp) cc_final: 0.7706 (mt) REVERT: A 131 CYS cc_start: 0.6843 (OUTLIER) cc_final: 0.6429 (m) REVERT: A 1136 THR cc_start: 0.8911 (OUTLIER) cc_final: 0.8685 (p) REVERT: B 844 ILE cc_start: 0.6794 (mt) cc_final: 0.6561 (mt) REVERT: C 787 GLN cc_start: 0.8553 (mm-40) cc_final: 0.7932 (mm-40) REVERT: C 1141 LEU cc_start: 0.6880 (mp) cc_final: 0.6608 (tp) outliers start: 33 outliers final: 25 residues processed: 212 average time/residue: 0.3568 time to fit residues: 122.7528 Evaluate side-chains 205 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 178 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 1100 THR Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 902 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 0.8980 chunk 271 optimal weight: 0.8980 chunk 59 optimal weight: 0.8980 chunk 177 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 301 optimal weight: 5.9990 chunk 250 optimal weight: 5.9990 chunk 139 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 158 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN A 925 ASN B 957 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 751 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.6503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 26097 Z= 0.179 Angle : 0.537 15.667 35515 Z= 0.276 Chirality : 0.045 0.255 4270 Planarity : 0.004 0.044 4491 Dihedral : 6.238 59.590 4994 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.83 % Favored : 97.13 % Rotamer: Outliers : 1.06 % Allowed : 12.03 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.15), residues: 3077 helix: 1.78 (0.20), residues: 700 sheet: 0.76 (0.20), residues: 628 loop : -1.17 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.003 0.001 HIS C 66 PHE 0.018 0.001 PHE C 168 TYR 0.016 0.001 TYR C1067 ARG 0.003 0.000 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 198 time to evaluate : 3.882 Fit side-chains revert: symmetry clash REVERT: A 100 ILE cc_start: 0.7929 (mp) cc_final: 0.7671 (mt) REVERT: A 131 CYS cc_start: 0.6720 (OUTLIER) cc_final: 0.6330 (m) REVERT: A 489 TYR cc_start: 0.8629 (m-80) cc_final: 0.8345 (m-80) REVERT: A 1136 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8731 (p) REVERT: C 489 TYR cc_start: 0.8369 (m-80) cc_final: 0.8167 (m-80) REVERT: C 690 GLN cc_start: 0.6538 (mm110) cc_final: 0.5758 (mm-40) REVERT: C 1141 LEU cc_start: 0.6804 (mp) cc_final: 0.6590 (tp) outliers start: 29 outliers final: 21 residues processed: 218 average time/residue: 0.4761 time to fit residues: 165.4979 Evaluate side-chains 204 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 181 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 902 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 220 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 254 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 chunk 300 optimal weight: 0.9990 chunk 188 optimal weight: 0.9980 chunk 183 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 164 ASN B 207 HIS B 957 GLN ** B1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 271 GLN C 474 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.6772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 26097 Z= 0.209 Angle : 0.552 15.367 35515 Z= 0.284 Chirality : 0.045 0.270 4270 Planarity : 0.004 0.045 4491 Dihedral : 6.181 57.582 4994 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.87 % Favored : 96.09 % Rotamer: Outliers : 1.10 % Allowed : 12.07 % Favored : 86.83 % 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: -0.04 (0.15), residues: 3077 helix: 1.79 (0.20), residues: 698 sheet: 0.71 (0.20), residues: 626 loop : -1.12 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 353 HIS 0.009 0.001 HIS B 207 PHE 0.020 0.001 PHE B 643 TYR 0.019 0.001 TYR C 756 ARG 0.002 0.000 ARG C 567 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 197 time to evaluate : 2.986 Fit side-chains revert: symmetry clash REVERT: A 100 ILE cc_start: 0.7919 (mp) cc_final: 0.7661 (mt) REVERT: A 319 ARG cc_start: 0.6865 (mtt180) cc_final: 0.6446 (mtt180) REVERT: C 489 TYR cc_start: 0.8477 (m-80) cc_final: 0.8267 (m-80) REVERT: C 613 GLN cc_start: 0.7989 (tt0) cc_final: 0.7768 (tt0) REVERT: C 690 GLN cc_start: 0.6654 (mm110) cc_final: 0.5821 (mm-40) outliers start: 30 outliers final: 26 residues processed: 217 average time/residue: 0.3536 time to fit residues: 124.5841 Evaluate side-chains 204 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 178 time to evaluate : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 94 SER Chi-restraints excluded: chain B residue 207 HIS Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 481 ASN Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 902 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 2.9990 chunk 120 optimal weight: 7.9990 chunk 179 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 191 optimal weight: 0.4980 chunk 204 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 236 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN B 164 ASN B 481 ASN B 935 GLN B 957 GLN B1101 HIS C 271 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.6844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 26097 Z= 0.185 Angle : 0.543 15.377 35515 Z= 0.279 Chirality : 0.045 0.321 4270 Planarity : 0.004 0.045 4491 Dihedral : 6.163 58.912 4994 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 2.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.06 % Favored : 96.91 % Rotamer: Outliers : 1.02 % Allowed : 12.40 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.15), residues: 3077 helix: 1.82 (0.20), residues: 699 sheet: 0.75 (0.20), residues: 628 loop : -1.09 (0.14), residues: 1750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.018 0.001 HIS B 207 PHE 0.021 0.001 PHE C 817 TYR 0.021 0.001 TYR A 904 ARG 0.003 0.000 ARG B 577 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6154 Ramachandran restraints generated. 3077 Oldfield, 0 Emsley, 3077 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 178 time to evaluate : 2.973 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ILE cc_start: 0.7912 (mp) cc_final: 0.7658 (mt) REVERT: C 14 GLN cc_start: 0.5204 (OUTLIER) cc_final: 0.4940 (mm-40) REVERT: C 489 TYR cc_start: 0.8461 (m-80) cc_final: 0.8254 (m-80) REVERT: C 613 GLN cc_start: 0.7981 (tt0) cc_final: 0.7761 (tt0) REVERT: C 690 GLN cc_start: 0.6589 (mm110) cc_final: 0.5770 (mm-40) REVERT: C 1125 ASN cc_start: 0.8095 (p0) cc_final: 0.7871 (p0) outliers start: 28 outliers final: 25 residues processed: 197 average time/residue: 0.3170 time to fit residues: 100.9302 Evaluate side-chains 198 residues out of total 2722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 172 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 137 ASN Chi-restraints excluded: chain A residue 274 THR Chi-restraints excluded: chain A residue 373 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 599 THR Chi-restraints excluded: chain B residue 605 SER Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 1050 MET Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain C residue 14 GLN Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 445 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 547 THR Chi-restraints excluded: chain C residue 551 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 902 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.7980 chunk 288 optimal weight: 3.9990 chunk 262 optimal weight: 8.9990 chunk 280 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 220 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 253 optimal weight: 0.9990 chunk 265 optimal weight: 0.7980 chunk 279 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: