Starting phenix.real_space_refine (version: dev) on Sun May 15 17:09:48 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1x_24126/05_2022/7n1x_24126.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1x_24126/05_2022/7n1x_24126.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1x_24126/05_2022/7n1x_24126.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1x_24126/05_2022/7n1x_24126.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1x_24126/05_2022/7n1x_24126.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n1x_24126/05_2022/7n1x_24126.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 sd= 0.044 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 654": "OE1" <-> "OE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 26810 Number of models: 1 Model: "" Number of chains: 35 Chain: "A" Number of atoms: 8434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8434 Classifications: {'peptide': 1077} Link IDs: {'PTRANS': 52, 'TRANS': 1024} Chain breaks: 5 Chain: "B" Number of atoms: 8522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1088, 8522 Classifications: {'peptide': 1088} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 52, 'TRANS': 1035} Chain breaks: 5 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 8554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1092, 8554 Classifications: {'peptide': 1092} Link IDs: {'PTRANS': 53, 'TRANS': 1038} Chain breaks: 4 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 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 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 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 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 chiralities: 2 Chain: "I" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'NAG': 2, 'FUC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'NAG': 2, 'MAN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'NAG': 2, 'MAN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 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 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 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 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 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 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 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 chiralities: 2 Chain: "S" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'NAG': 2, 'FUC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "T" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'NAG': 2, 'MAN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "U" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'NAG': 2, 'MAN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 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 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 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 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 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 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 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 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 chiralities: 2 Chain: "d" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'NAG': 2, 'FUC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "e" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'NAG': 2, 'MAN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'NAG': 2, 'MAN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 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 chiralities: 8 Time building chain proxies: 15.50, per 1000 atoms: 0.58 Number of scatterers: 26810 At special positions: 0 Unit cell: (155.938, 154.288, 216.168, 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 5321 8.00 N 4338 7.00 C 17037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.04 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=2.02 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=2.06 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=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.01 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.05 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=2.02 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.06 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.04 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=2.04 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=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.04 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.00 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.05 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.05 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.06 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.01 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=2.02 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=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.04 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 ALPHA1-4 " NAG J 2 " - " MAN J 3 " " NAG K 2 " - " MAN K 3 " " NAG T 2 " - " MAN T 3 " " NAG U 2 " - " MAN U 3 " " NAG e 2 " - " MAN e 3 " " NAG f 2 " - " MAN f 3 " 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 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 " BETA1-6 " NAG I 1 " - " FUC I 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG S 1 " - " FUC S 3 " " NAG d 1 " - " FUC d 3 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 149 " " NAG A1404 " - " ASN A 165 " " NAG A1405 " - " ASN A 234 " " NAG A1406 " - " ASN A 282 " " NAG A1407 " - " ASN A 343 " " NAG A1408 " - " ASN A 603 " " NAG A1409 " - " ASN A 657 " " NAG A1410 " - " ASN A 709 " " NAG A1411 " - " ASN A1158 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 149 " " NAG B1403 " - " ASN B 234 " " NAG B1404 " - " ASN B 331 " " NAG B1405 " - " ASN B 343 " " NAG B1406 " - " ASN B 603 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B 709 " " NAG B1409 " - " ASN B1158 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 149 " " NAG C1403 " - " ASN C 331 " " NAG C1404 " - " ASN C 343 " " NAG C1406 " - " ASN C 657 " " NAG C1407 " - " ASN C 709 " " NAG C1408 " - " ASN C1158 " " NAG D 1 " - " ASN A 17 " " NAG E 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 717 " " NAG H 1 " - " ASN A 801 " " NAG I 1 " - " ASN A1074 " " NAG J 1 " - " ASN A1098 " " NAG K 1 " - " ASN A1134 " " NAG L 1 " - " ASN B 17 " " NAG M 1 " - " ASN B 122 " " NAG N 1 " - " ASN B 165 " " NAG O 1 " - " ASN B 282 " " NAG P 1 " - " ASN B 616 " " NAG Q 1 " - " ASN B 717 " " NAG R 1 " - " ASN B 801 " " NAG S 1 " - " ASN B1074 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 17 " " NAG W 1 " - " ASN C 122 " " NAG X 1 " - " ASN C 165 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 282 " " NAG a 1 " - " ASN C 616 " " NAG b 1 " - " ASN C 717 " " NAG c 1 " - " ASN C 801 " " NAG d 1 " - " ASN C1074 " " NAG e 1 " - " ASN C1098 " " NAG f 1 " - " ASN C1134 " Time building additional restraints: 11.95 Conformation dependent library (CDL) restraints added in 4.3 seconds 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6102 Finding SS restraints... Secondary structure from input PDB file: 77 helices and 48 sheets defined 26.3% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 337 through 342 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 368 removed outlier: 4.646A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.516A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.638A pdb=" N ILE A 410 " --> pdb=" O VAL A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 755 Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.931A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LYS A 776 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 801 through 805 removed outlier: 4.119A pdb=" N GLN A 804 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.614A pdb=" N LEU A 821 " --> pdb=" O PHE A 817 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A 823 " --> pdb=" O GLU A 819 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 854 through 856 No H-bonds generated for 'chain 'A' and resid 854 through 856' Processing helix chain 'A' and resid 866 through 882 Processing helix chain 'A' and resid 886 through 891 removed outlier: 3.775A pdb=" N ALA A 890 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 913 through 918 Processing helix chain 'A' and resid 919 through 941 removed outlier: 3.570A pdb=" N SER A 929 " --> pdb=" O ASN A 925 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER A 940 " --> pdb=" O ASP A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.794A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN A 954 " --> pdb=" O ASP A 950 " (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 977 through 982 Processing helix chain 'A' and resid 989 through 1033 removed outlier: 3.999A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1141 through 1161 removed outlier: 3.853A pdb=" N LYS A1149 " --> pdb=" O LEU A1145 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU A1152 " --> pdb=" O PHE A1148 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.092A 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: 3.878A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 411 removed outlier: 5.447A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 618 through 623 removed outlier: 4.013A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 639 removed outlier: 3.672A pdb=" N GLY B 639 " --> pdb=" O TYR B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 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 760 through 783 removed outlier: 3.808A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 801 through 805 removed outlier: 3.570A pdb=" N GLN B 804 " --> pdb=" O ASN B 801 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 824 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.633A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 removed outlier: 3.568A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 938 " --> pdb=" O ILE B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.258A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 958 " --> pdb=" O GLN B 954 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 978 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.003A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1118 No H-bonds generated for 'chain 'B' and resid 1116 through 1118' Processing helix chain 'B' and resid 1140 through 1161 removed outlier: 3.510A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N SER B1147 " --> pdb=" O PRO B1143 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU B1151 " --> pdb=" O SER B1147 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B1161 " --> pdb=" O LYS B1157 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 removed outlier: 3.675A pdb=" N THR C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.046A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 386 through 389 Processing helix chain 'C' and resid 406 through 411 removed outlier: 3.531A pdb=" N ILE C 410 " --> pdb=" O GLU C 406 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA C 411 " --> pdb=" O VAL C 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 406 through 411' Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 438 through 443 Processing helix chain 'C' and resid 616 through 620 removed outlier: 3.665A pdb=" N VAL C 620 " --> pdb=" O CYS C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 639 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 747 through 755 removed outlier: 3.614A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.620A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 801 through 805 removed outlier: 4.516A pdb=" N GLN C 804 " --> pdb=" O ASN C 801 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.585A pdb=" N LEU C 821 " --> pdb=" O PHE C 817 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN C 824 " --> pdb=" O ASP C 820 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.731A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 907 Processing helix chain 'C' and resid 908 through 910 No H-bonds generated for 'chain 'C' and resid 908 through 910' Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.582A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 Processing helix chain 'C' and resid 942 through 944 No H-bonds generated for 'chain 'C' and resid 942 through 944' Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.758A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (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 removed outlier: 3.555A pdb=" N ILE C 980 " --> pdb=" O VAL C 976 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.167A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1159 removed outlier: 4.134A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 3.789A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA A 263 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS A 187 " --> pdb=" O ILE A 210 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 197 " --> pdb=" O TYR A 200 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.228A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 8.889A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 11.218A pdb=" N SER A 221 " --> pdb=" O PRO A 209 " (cutoff:3.500A) removed outlier: 6.095A pdb=" N ARG A 34 " --> pdb=" O SER A 221 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N LEU A 223 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.148A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.562A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 13.353A pdb=" N PHE A 135 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 13.045A pdb=" N THR A 240 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 10.614A pdb=" N ASN A 137 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 10.276A pdb=" N LEU A 242 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N LEU A 244 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 8.399A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.109A pdb=" N ARG A 237 " --> pdb=" O PHE A 106 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N PHE A 106 " --> pdb=" O ARG A 237 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N GLN A 239 " --> pdb=" O TRP A 104 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N TRP A 104 " --> pdb=" O GLN A 239 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU A 241 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 4.780A pdb=" N ASN A 317 " --> pdb=" O GLY A 593 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLY A 593 " --> pdb=" O ASN A 317 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.525A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.769A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.769A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.451A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) 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 473 through 474 Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.424A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 701 through 704 Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.256A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA A1056 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.256A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASN A 717 " --> pdb=" O ALA A1070 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 735 through 736 Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 790 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 3.503A pdb=" N SER A1123 " --> pdb=" O ALA A1087 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 removed outlier: 9.249A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS B 187 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N HIS B 207 " --> pdb=" O ALA B 222 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N ALA B 222 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 7.244A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 6.077A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE B 168 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N GLU B 132 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N CYS B 166 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 10.179A pdb=" N GLN B 134 " --> pdb=" O ASN B 164 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N ASN B 164 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 8.634A pdb=" N CYS B 136 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 10.412A pdb=" N SER B 162 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N ASP B 138 " --> pdb=" O TYR B 160 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N TYR B 160 " --> pdb=" O ASP B 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.212A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 324 through 328 removed outlier: 6.953A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ASN B 542 " --> pdb=" O GLU B 324 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE B 326 " --> pdb=" O ASN B 542 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.811A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 361 through 362 removed outlier: 7.220A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.334A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.551A pdb=" N GLN B1071 " --> pdb=" O ILE B 716 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD6, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.243A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 1094 through 1097 Processing sheet with id=AD8, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.765A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 8.459A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ALA C 264 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N THR C 95 " --> pdb=" O ALA C 264 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N LYS C 187 " --> pdb=" O ILE C 210 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.070A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.621A pdb=" N ASP C 53 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.352A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE C 168 " --> pdb=" O VAL C 130 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 133 through 135 removed outlier: 6.627A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 142 through 144 removed outlier: 6.300A pdb=" N GLY C 142 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET C 153 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.090A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.308A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 7.181A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.371A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.514A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.514A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN C 717 " --> pdb=" O ALA C1070 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.447A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.416A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1063 hydrogen bonds defined for protein. 2898 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: 12.83 Time building geometry restraints manager: 12.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 4356 1.30 - 1.43: 7337 1.43 - 1.56: 15563 1.56 - 1.70: 4 1.70 - 1.83: 144 Bond restraints: 27404 Sorted by residual: bond pdb=" C4 NAG U 2 " pdb=" O4 NAG U 2 " ideal model delta sigma weight residual 1.423 1.486 -0.063 1.00e-02 1.00e+04 3.94e+01 bond pdb=" C4 NAG K 2 " pdb=" O4 NAG K 2 " ideal model delta sigma weight residual 1.423 1.485 -0.062 1.00e-02 1.00e+04 3.87e+01 bond pdb=" C5 NAG J 2 " pdb=" O5 NAG J 2 " ideal model delta sigma weight residual 1.435 1.502 -0.067 1.10e-02 8.26e+03 3.71e+01 bond pdb=" C4 NAG T 2 " pdb=" O4 NAG T 2 " ideal model delta sigma weight residual 1.423 1.482 -0.059 1.00e-02 1.00e+04 3.44e+01 bond pdb=" C4 NAG O 1 " pdb=" O4 NAG O 1 " ideal model delta sigma weight residual 1.423 1.482 -0.059 1.00e-02 1.00e+04 3.42e+01 ... (remaining 27399 not shown) Histogram of bond angle deviations from ideal: 96.49 - 104.42: 363 104.42 - 112.34: 11948 112.34 - 120.27: 14252 120.27 - 128.19: 10611 128.19 - 136.11: 104 Bond angle restraints: 37278 Sorted by residual: angle pdb=" OD1 ASN C 61 " pdb=" CG ASN C 61 " pdb=" ND2 ASN C 61 " ideal model delta sigma weight residual 122.60 114.14 8.46 1.00e+00 1.00e+00 7.15e+01 angle pdb=" OD1 ASN B 331 " pdb=" CG ASN B 331 " pdb=" ND2 ASN B 331 " ideal model delta sigma weight residual 122.60 114.92 7.68 1.00e+00 1.00e+00 5.90e+01 angle pdb=" CB ASN C 61 " pdb=" CG ASN C 61 " pdb=" ND2 ASN C 61 " ideal model delta sigma weight residual 116.40 127.55 -11.15 1.50e+00 4.44e-01 5.53e+01 angle pdb=" CB ASN B 331 " pdb=" CG ASN B 331 " pdb=" ND2 ASN B 331 " ideal model delta sigma weight residual 116.40 127.25 -10.85 1.50e+00 4.44e-01 5.24e+01 angle pdb=" CA ASP A 570 " pdb=" CB ASP A 570 " pdb=" CG ASP A 570 " ideal model delta sigma weight residual 112.60 119.67 -7.07 1.00e+00 1.00e+00 5.00e+01 ... (remaining 37273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.02: 15266 23.02 - 46.04: 716 46.04 - 69.05: 127 69.05 - 92.07: 55 92.07 - 115.09: 5 Dihedral angle restraints: 16169 sinusoidal: 6684 harmonic: 9485 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -155.73 69.73 1 1.00e+01 1.00e-02 6.27e+01 dihedral pdb=" CB CYS A 15 " pdb=" SG CYS A 15 " pdb=" SG CYS A 136 " pdb=" CB CYS A 136 " ideal model delta sinusoidal sigma weight residual 93.00 156.66 -63.66 1 1.00e+01 1.00e-02 5.34e+01 dihedral pdb=" CA GLY B 526 " pdb=" C GLY B 526 " pdb=" N PRO B 527 " pdb=" CA PRO B 527 " ideal model delta harmonic sigma weight residual -180.00 -150.25 -29.75 0 5.00e+00 4.00e-02 3.54e+01 ... (remaining 16166 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.684: 4477 0.684 - 1.369: 6 1.369 - 2.053: 1 2.053 - 2.738: 3 2.738 - 3.422: 1 Chirality restraints: 4488 Sorted by residual: chirality pdb=" C1 NAG A1402 " pdb=" ND2 ASN A 122 " pdb=" C2 NAG A1402 " pdb=" O5 NAG A1402 " both_signs ideal model delta sigma weight residual False -2.40 1.02 -3.42 2.00e-01 2.50e+01 2.93e+02 chirality pdb=" C1 NAG B1405 " pdb=" ND2 ASN B 343 " pdb=" C2 NAG B1405 " pdb=" O5 NAG B1405 " both_signs ideal model delta sigma weight residual False -2.40 0.32 -2.72 2.00e-01 2.50e+01 1.85e+02 chirality pdb=" C1 NAG X 1 " pdb=" ND2 ASN C 165 " pdb=" C2 NAG X 1 " pdb=" O5 NAG X 1 " both_signs ideal model delta sigma weight residual False -2.40 0.20 -2.60 2.00e-01 2.50e+01 1.69e+02 ... (remaining 4485 not shown) Planarity restraints: 4745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.343 2.00e-02 2.50e+03 3.70e-01 1.71e+03 pdb=" CG ASN A 343 " 0.119 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.030 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.614 2.00e-02 2.50e+03 pdb=" C1 NAG A1407 " -0.420 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 343 " -0.279 2.00e-02 2.50e+03 2.99e-01 1.12e+03 pdb=" CG ASN B 343 " 0.102 2.00e-02 2.50e+03 pdb=" OD1 ASN B 343 " 0.052 2.00e-02 2.50e+03 pdb=" ND2 ASN B 343 " 0.479 2.00e-02 2.50e+03 pdb=" C1 NAG B1405 " -0.354 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 17 " -0.243 2.00e-02 2.50e+03 2.41e-01 7.29e+02 pdb=" CG ASN B 17 " 0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN B 17 " 0.062 2.00e-02 2.50e+03 pdb=" ND2 ASN B 17 " 0.381 2.00e-02 2.50e+03 pdb=" C1 NAG L 1 " -0.277 2.00e-02 2.50e+03 ... (remaining 4742 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.17: 18 2.17 - 2.85: 7546 2.85 - 3.53: 37581 3.53 - 4.22: 63806 4.22 - 4.90: 105353 Nonbonded interactions: 214304 Sorted by model distance: nonbonded pdb=" NH2 ARG B 905 " pdb=" O LEU B1049 " model vdw 1.484 2.520 nonbonded pdb=" O MET B 900 " pdb=" CD2 TYR B 904 " model vdw 1.609 3.340 nonbonded pdb=" O HIS C 66 " pdb=" NH1 ARG C 78 " model vdw 1.711 2.520 nonbonded pdb=" OE1 GLU B 132 " pdb=" ND2 ASN B 165 " model vdw 1.725 2.520 nonbonded pdb=" NH1 ARG A 457 " pdb=" OD2 ASP A 467 " model vdw 1.823 2.520 ... (remaining 214299 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 14 through 826 or resid 855 through 1162 or resid 1401 thr \ ough 1408)) selection = (chain 'B' and (resid 14 through 623 or resid 641 through 826 or resid 855 throu \ gh 1162 or resid 1401 through 1408)) selection = (chain 'C' and (resid 14 through 623 or resid 641 through 826 or resid 855 throu \ gh 1162 or resid 1401 through 1408)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' } ncs_group { reference = (chain 'I' and resid 1 through 2) selection = (chain 'J' and resid 1 through 2) selection = (chain 'K' and resid 1 through 2) selection = (chain 'S' and resid 1 through 2) selection = (chain 'T' and resid 1 through 2) selection = (chain 'U' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'e' and resid 1 through 2) selection = (chain 'f' and resid 1 through 2) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 114 5.16 5 C 17037 2.51 5 N 4338 2.21 5 O 5321 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 5.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 26.030 Check model and map are aligned: 0.450 Convert atoms to be neutral: 0.260 Process input model: 74.850 Find NCS groups from input model: 2.420 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 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 : 0.013 0.077 27404 Z= 0.868 Angle : 1.879 13.022 37278 Z= 1.257 Chirality : 0.140 3.422 4488 Planarity : 0.014 0.120 4690 Dihedral : 14.656 115.090 9941 Min Nonbonded Distance : 1.484 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.13 % Favored : 91.25 % Rotamer Outliers : 1.97 % Cbeta Deviations : 0.43 % 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: -2.39 (0.13), residues: 3223 helix: -2.19 (0.16), residues: 704 sheet: -0.17 (0.21), residues: 546 loop : -1.83 (0.13), residues: 1973 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 797 time to evaluate : 3.058 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 19 residues processed: 834 average time/residue: 0.3905 time to fit residues: 506.2661 Evaluate side-chains 627 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 608 time to evaluate : 3.110 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2775 time to fit residues: 13.9603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 0.9990 chunk 245 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 165 optimal weight: 1.9990 chunk 131 optimal weight: 0.6980 chunk 253 optimal weight: 0.4980 chunk 98 optimal weight: 3.9990 chunk 154 optimal weight: 0.9980 chunk 189 optimal weight: 0.8980 chunk 294 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 99 ASN A 580 GLN A 655 HIS A 751 ASN A 804 GLN A 901 GLN A 926 GLN A 935 GLN A 954 GLN A 957 GLN A 965 GLN A1005 GLN B 317 ASN ** B 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 644 GLN B 762 GLN B 925 ASN B 954 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1036 GLN C 52 GLN C 360 ASN C 487 ASN C 935 GLN C 954 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.112 27404 Z= 0.271 Angle : 0.814 13.797 37278 Z= 0.439 Chirality : 0.057 1.042 4488 Planarity : 0.005 0.087 4690 Dihedral : 8.791 114.073 4093 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.53 % Rotamer Outliers : 3.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.52 (0.14), residues: 3223 helix: -0.51 (0.18), residues: 713 sheet: -0.31 (0.20), residues: 634 loop : -1.48 (0.13), residues: 1876 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 625 time to evaluate : 3.122 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 44 residues processed: 671 average time/residue: 0.3977 time to fit residues: 423.8829 Evaluate side-chains 594 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 550 time to evaluate : 3.154 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 44 outliers final: 1 residues processed: 44 average time/residue: 0.2595 time to fit residues: 25.4475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 244 optimal weight: 3.9990 chunk 200 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 294 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 292 optimal weight: 3.9990 chunk 100 optimal weight: 0.1980 chunk 236 optimal weight: 0.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 173 GLN A 493 GLN A 580 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A1005 GLN ** A1083 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 GLN B 164 ASN B 394 ASN B 409 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN B 856 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B1036 GLN C 52 GLN C 271 GLN C 360 ASN C 603 ASN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C1036 GLN C1054 GLN C1058 HIS C1106 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.128 27404 Z= 0.302 Angle : 0.761 11.194 37278 Z= 0.403 Chirality : 0.053 0.806 4488 Planarity : 0.005 0.082 4690 Dihedral : 8.402 112.203 4093 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer Outliers : 3.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.14), residues: 3223 helix: -0.09 (0.19), residues: 724 sheet: -0.45 (0.20), residues: 632 loop : -1.46 (0.13), residues: 1867 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 585 time to evaluate : 3.118 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: symmetry clash outliers start: 88 outliers final: 52 residues processed: 636 average time/residue: 0.4057 time to fit residues: 413.9388 Evaluate side-chains 585 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 533 time to evaluate : 3.378 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 52 outliers final: 1 residues processed: 52 average time/residue: 0.2722 time to fit residues: 29.8422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 0.0770 chunk 221 optimal weight: 0.8980 chunk 152 optimal weight: 0.0770 chunk 32 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 295 optimal weight: 0.9980 chunk 313 optimal weight: 0.7980 chunk 154 optimal weight: 0.9980 chunk 280 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN A 613 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 914 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B 856 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 474 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.122 27404 Z= 0.224 Angle : 0.692 12.093 37278 Z= 0.363 Chirality : 0.050 0.645 4488 Planarity : 0.005 0.084 4690 Dihedral : 8.003 108.801 4093 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 2.21 % 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: -1.20 (0.14), residues: 3223 helix: 0.33 (0.20), residues: 718 sheet: -0.47 (0.20), residues: 616 loop : -1.38 (0.13), residues: 1889 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 586 time to evaluate : 3.221 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 63 outliers final: 35 residues processed: 615 average time/residue: 0.3949 time to fit residues: 388.3859 Evaluate side-chains 562 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 527 time to evaluate : 3.379 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 35 outliers final: 1 residues processed: 35 average time/residue: 0.2388 time to fit residues: 20.1390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 4.9990 chunk 177 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 233 optimal weight: 5.9990 chunk 129 optimal weight: 0.0010 chunk 267 optimal weight: 3.9990 chunk 216 optimal weight: 0.0570 chunk 0 optimal weight: 7.9990 chunk 159 optimal weight: 4.9990 chunk 281 optimal weight: 0.2980 chunk 79 optimal weight: 4.9990 overall best weight: 0.8706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 613 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 969 ASN B 164 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 755 GLN B 787 GLN B 925 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6897 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.125 27404 Z= 0.258 Angle : 0.703 10.790 37278 Z= 0.367 Chirality : 0.049 0.540 4488 Planarity : 0.005 0.089 4690 Dihedral : 7.913 106.336 4093 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer Outliers : 2.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.14), residues: 3223 helix: 0.43 (0.20), residues: 717 sheet: -0.56 (0.20), residues: 621 loop : -1.42 (0.13), residues: 1885 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 641 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 572 time to evaluate : 3.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 32 residues processed: 614 average time/residue: 0.3822 time to fit residues: 374.7040 Evaluate side-chains 564 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 532 time to evaluate : 3.291 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.2694 time to fit residues: 20.6864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 0.8980 chunk 282 optimal weight: 2.9990 chunk 61 optimal weight: 0.0570 chunk 183 optimal weight: 0.2980 chunk 77 optimal weight: 0.8980 chunk 313 optimal weight: 0.9980 chunk 260 optimal weight: 0.3980 chunk 145 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 103 optimal weight: 0.9990 chunk 164 optimal weight: 0.8980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 787 GLN B 955 ASN B 957 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS C 360 ASN C 487 ASN C 779 GLN C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN ** C1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.3874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.125 27404 Z= 0.212 Angle : 0.680 11.673 37278 Z= 0.352 Chirality : 0.049 0.503 4488 Planarity : 0.005 0.092 4690 Dihedral : 7.726 104.041 4093 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer Outliers : 1.83 % 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: -1.08 (0.14), residues: 3223 helix: 0.65 (0.20), residues: 712 sheet: -0.58 (0.19), residues: 636 loop : -1.34 (0.14), residues: 1875 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 566 time to evaluate : 3.190 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 outliers start: 52 outliers final: 24 residues processed: 589 average time/residue: 0.3827 time to fit residues: 359.7773 Evaluate side-chains 549 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 525 time to evaluate : 3.186 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.2473 time to fit residues: 15.9216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 chunk 178 optimal weight: 0.5980 chunk 228 optimal weight: 0.0040 chunk 177 optimal weight: 0.6980 chunk 263 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 312 optimal weight: 1.9990 chunk 195 optimal weight: 0.8980 chunk 190 optimal weight: 0.8980 chunk 144 optimal weight: 0.2980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 824 ASN A 901 GLN A1054 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN ** B 901 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 957 GLN B 969 ASN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN C1054 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1142 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.175 27404 Z= 0.215 Angle : 0.680 14.495 37278 Z= 0.352 Chirality : 0.048 0.464 4488 Planarity : 0.005 0.099 4690 Dihedral : 7.613 101.841 4093 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.14), residues: 3223 helix: 0.76 (0.20), residues: 714 sheet: -0.50 (0.20), residues: 631 loop : -1.29 (0.14), residues: 1878 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 555 time to evaluate : 3.100 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 outliers start: 45 outliers final: 19 residues processed: 579 average time/residue: 0.3852 time to fit residues: 357.3467 Evaluate side-chains 544 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 525 time to evaluate : 2.842 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.2439 time to fit residues: 12.5395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 186 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 198 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 245 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 ASN A 613 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 GLN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 314 GLN ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 703 ASN B 755 GLN B 957 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 779 GLN C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 960 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.274 27404 Z= 0.272 Angle : 0.716 18.301 37278 Z= 0.374 Chirality : 0.049 0.448 4488 Planarity : 0.005 0.120 4690 Dihedral : 7.700 103.504 4093 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 0.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.14), residues: 3223 helix: 0.75 (0.20), residues: 707 sheet: -0.54 (0.20), residues: 626 loop : -1.37 (0.14), residues: 1890 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 539 time to evaluate : 2.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 555 average time/residue: 0.3823 time to fit residues: 337.5890 Evaluate side-chains 524 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 514 time to evaluate : 3.116 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2398 time to fit residues: 8.7964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 0.6980 chunk 299 optimal weight: 0.8980 chunk 272 optimal weight: 0.0020 chunk 291 optimal weight: 0.8980 chunk 175 optimal weight: 0.9990 chunk 126 optimal weight: 4.9990 chunk 228 optimal weight: 0.0870 chunk 89 optimal weight: 0.6980 chunk 262 optimal weight: 4.9990 chunk 275 optimal weight: 0.9990 chunk 289 optimal weight: 1.9990 overall best weight: 0.4766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 703 ASN B 755 GLN B 955 ASN B 957 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 926 GLN ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.4354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.460 27404 Z= 0.262 Angle : 0.727 26.637 37278 Z= 0.380 Chirality : 0.048 0.444 4488 Planarity : 0.006 0.123 4690 Dihedral : 7.580 101.288 4093 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.14), residues: 3223 helix: 0.81 (0.20), residues: 704 sheet: -0.52 (0.20), residues: 631 loop : -1.31 (0.14), residues: 1888 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 537 time to evaluate : 3.273 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 outliers start: 17 outliers final: 6 residues processed: 542 average time/residue: 0.3972 time to fit residues: 346.4979 Evaluate side-chains 525 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 519 time to evaluate : 3.126 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2390 time to fit residues: 6.8872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 1.9990 chunk 307 optimal weight: 0.9990 chunk 187 optimal weight: 3.9990 chunk 145 optimal weight: 4.9990 chunk 213 optimal weight: 0.0970 chunk 322 optimal weight: 2.9990 chunk 297 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 chunk 157 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 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 777 ASN ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 703 ASN B 755 GLN B 957 GLN ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.441 27404 Z= 0.355 Angle : 0.878 73.890 37278 Z= 0.437 Chirality : 0.050 0.545 4488 Planarity : 0.006 0.133 4690 Dihedral : 7.592 101.531 4093 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.75 % Favored : 95.22 % Rotamer Outliers : 0.42 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.01 (0.14), residues: 3223 helix: 0.78 (0.20), residues: 704 sheet: -0.52 (0.20), residues: 633 loop : -1.32 (0.14), residues: 1886 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6446 Ramachandran restraints generated. 3223 Oldfield, 0 Emsley, 3223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 518 time to evaluate : 4.690 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 outliers start: 12 outliers final: 7 residues processed: 527 average time/residue: 0.4034 time to fit residues: 342.8698 Evaluate side-chains 516 residues out of total 2848 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 509 time to evaluate : 2.866 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.2561 time to fit residues: 7.2998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 0.9980 chunk 273 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 237 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 71 optimal weight: 2.9990 chunk 257 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 264 optimal weight: 0.1980 chunk 32 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 613 GLN ** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 926 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1036 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 703 ASN B 755 GLN B 777 ASN B 957 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 542 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.086191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.070925 restraints weight = 107259.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.073015 restraints weight = 59858.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.074391 restraints weight = 39278.962| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 moved from start: 0.4464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.768 27404 Z= 0.337 Angle : 0.825 57.146 37278 Z= 0.425 Chirality : 0.049 0.441 4488 Planarity : 0.006 0.135 4690 Dihedral : 7.585 101.589 4093 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.14), residues: 3223 helix: 0.86 (0.20), residues: 697 sheet: -0.64 (0.20), residues: 647 loop : -1.32 (0.14), residues: 1879 =============================================================================== Job complete usr+sys time: 7028.88 seconds wall clock time: 128 minutes 1.89 seconds (7681.89 seconds total)