Starting phenix.real_space_refine on Mon Nov 20 16:11:17 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtq_34263/11_2023/8gtq_34263.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtq_34263/11_2023/8gtq_34263.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtq_34263/11_2023/8gtq_34263.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtq_34263/11_2023/8gtq_34263.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtq_34263/11_2023/8gtq_34263.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gtq_34263/11_2023/8gtq_34263.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.089 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 135 5.16 5 C 19449 2.51 5 N 4980 2.21 5 O 5955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A ARG 158": "NH1" <-> "NH2" Residue "A PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 198": "OD1" <-> "OD2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A ARG 346": "NH1" <-> "NH2" Residue "A ARG 355": "NH1" <-> "NH2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 403": "NH1" <-> "NH2" Residue "A GLU 661": "OE1" <-> "OE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B ARG 158": "NH1" <-> "NH2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 281": "OE1" <-> "OE2" Residue "B ARG 319": "NH1" <-> "NH2" Residue "B GLU 324": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 346": "NH1" <-> "NH2" Residue "B ARG 355": "NH1" <-> "NH2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 403": "NH1" <-> "NH2" Residue "B GLU 661": "OE1" <-> "OE2" Residue "C TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C ARG 158": "NH1" <-> "NH2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 214": "NH1" <-> "NH2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C ARG 319": "NH1" <-> "NH2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 346": "NH1" <-> "NH2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H ARG 103": "NH1" <-> "NH2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "I GLU 89": "OE1" <-> "OE2" Residue "I ARG 103": "NH1" <-> "NH2" Residue "M PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 81": "OE1" <-> "OE2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J ARG 103": "NH1" <-> "NH2" Residue "N PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 81": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 30519 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "B" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "C" Number of atoms: 8043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8043 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 948 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "I" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 948 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "M" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "J" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 948 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain: "N" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 832 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 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: 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: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 140 Unusual residues: {'NAG': 10} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 16.30, per 1000 atoms: 0.53 Number of scatterers: 30519 At special positions: 0 Unit cell: (152.934, 157.242, 192.783, 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 135 16.00 O 5955 8.00 N 4980 7.00 C 19449 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.08 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.11 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=2.02 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=1.89 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=1.99 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.26 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=1.97 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.17 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.10 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.08 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=1.56 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.02 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=1.98 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=1.99 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.26 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=1.97 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.17 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.10 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.08 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=1.91 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.02 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.02 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.10 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=1.99 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.26 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=1.97 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.17 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.10 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 23 " - pdb=" SG CYS M 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 23 " - pdb=" SG CYS N 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A1409 " - " NAG A1410 " " NAG B1409 " - " NAG B1410 " " NAG C1409 " - " NAG C1410 " " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " NAG D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG K 1 " - " NAG K 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " NAG Q 3 " " 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 X 2 " - " NAG X 3 " " 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-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 282 " " NAG A1405 " - " ASN A 603 " " NAG A1406 " - " ASN A 616 " " NAG A1407 " - " ASN A 657 " " NAG A1408 " - " ASN A 709 " " NAG A1409 " - " ASN A1074 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 282 " " NAG B1405 " - " ASN B 603 " " NAG B1406 " - " ASN B 616 " " NAG B1407 " - " ASN B 657 " " NAG B1408 " - " ASN B 709 " " NAG B1409 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 282 " " NAG C1405 " - " ASN C 603 " " NAG C1406 " - " ASN C 616 " " NAG C1407 " - " ASN C 657 " " NAG C1408 " - " ASN C 709 " " NAG C1409 " - " ASN C1074 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 331 " " NAG F 1 " - " ASN A 343 " " NAG G 1 " - " ASN A 717 " " NAG K 1 " - " ASN A 801 " " NAG O 1 " - " ASN A1098 " " NAG P 1 " - " ASN A1134 " " NAG Q 1 " - " ASN B 234 " " NAG R 1 " - " ASN B 331 " " NAG S 1 " - " ASN B 343 " " NAG T 1 " - " ASN B 717 " " NAG U 1 " - " ASN B 801 " " NAG V 1 " - " ASN B1098 " " NAG W 1 " - " ASN B1134 " " NAG X 1 " - " ASN C 234 " " NAG Y 1 " - " ASN C 331 " " NAG Z 1 " - " ASN C 343 " " NAG a 1 " - " ASN C 717 " " NAG b 1 " - " ASN C 801 " " NAG c 1 " - " ASN C1098 " " NAG d 1 " - " ASN C1134 " Time building additional restraints: 12.79 Conformation dependent library (CDL) restraints added in 5.7 seconds 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6996 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 57 sheets defined 19.3% alpha, 31.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 295 through 304 Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.531A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 390 removed outlier: 3.918A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 410 removed outlier: 3.654A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER A 408 " --> pdb=" O ASN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 754 removed outlier: 4.088A pdb=" N ASN A 751 " --> pdb=" O THR A 747 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.987A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 823 removed outlier: 3.590A pdb=" N LEU A 821 " --> pdb=" O PRO A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.513A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.576A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.652A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.590A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 4.080A pdb=" N ILE A 934 " --> pdb=" O ALA A 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.756A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 978 through 983 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.324A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1145 Processing helix chain 'B' and resid 294 through 304 removed outlier: 3.930A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 removed outlier: 3.532A pdb=" N ASN B 370 " --> pdb=" O SER B 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 390 removed outlier: 3.919A pdb=" N LEU B 387 " --> pdb=" O PRO B 384 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.654A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 747 through 754 removed outlier: 4.087A pdb=" N ASN B 751 " --> pdb=" O THR B 747 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU B 752 " --> pdb=" O GLU B 748 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.986A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 removed outlier: 3.590A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.513A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY B 889 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 removed outlier: 3.651A pdb=" N ILE B 909 " --> pdb=" O ARG B 905 " (cutoff:3.500A) Processing helix chain 'B' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE B 934 " --> pdb=" O ALA B 930 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN B 935 " --> pdb=" O ILE B 931 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP B 936 " --> pdb=" O GLY B 932 " (cutoff:3.500A) Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 978 through 983 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.323A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B1033 " --> pdb=" O MET B1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 1140 through 1145 Processing helix chain 'C' and resid 295 through 304 Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.532A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.919A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU C 390 " --> pdb=" O LEU C 387 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 410 removed outlier: 3.653A pdb=" N VAL C 407 " --> pdb=" O GLY C 404 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N SER C 408 " --> pdb=" O ASN C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 747 through 754 removed outlier: 4.087A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LEU C 752 " --> pdb=" O GLU C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.986A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 removed outlier: 3.591A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 removed outlier: 3.514A pdb=" N THR C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 886 through 890 removed outlier: 3.577A pdb=" N GLY C 889 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.650A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 918 removed outlier: 3.591A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 939 removed outlier: 4.078A pdb=" N ILE C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN C 935 " --> pdb=" O ILE C 931 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.757A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 978 through 983 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.323A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C1033 " --> pdb=" O MET C1029 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1145 Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.563A pdb=" N ASP H 90 " --> pdb=" O ARG H 87 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR H 91 " --> pdb=" O ALA H 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 87 through 91' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.853A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 91 removed outlier: 3.562A pdb=" N ASP I 90 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR I 91 " --> pdb=" O ALA I 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 87 through 91' Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.853A pdb=" N ILE M 83 " --> pdb=" O PRO M 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 91 removed outlier: 3.563A pdb=" N ASP J 90 " --> pdb=" O ARG J 87 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR J 91 " --> pdb=" O ALA J 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 87 through 91' Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.852A pdb=" N ILE N 83 " --> pdb=" O PRO N 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 7.076A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 5.815A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN A 164 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL A 120 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.575A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLN A 613 " --> pdb=" O GLY A 594 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER A 596 " --> pdb=" O LEU A 611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU A 611 " --> pdb=" O SER A 596 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.547A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.695A pdb=" N TYR A 473 " --> pdb=" O TYR A 489 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'A' and resid 538 through 543 removed outlier: 5.815A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 670 through 674 removed outlier: 3.935A pdb=" N ILE A 693 " --> pdb=" O SER A 673 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 702 through 704 removed outlier: 3.868A pdb=" N LYS B 790 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.152A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 7.152A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N THR A 724 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU A1063 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ILE A 726 " --> pdb=" O VAL A1061 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL A1061 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY A1059 " --> pdb=" O PRO A 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.666A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.945A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 28 through 31 removed outlier: 3.701A pdb=" N ILE B 203 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL B 227 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.012A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.504A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN B 164 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.504A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 310 through 317 removed outlier: 5.056A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.546A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.695A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 538 through 543 removed outlier: 5.815A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 654 through 656 removed outlier: 6.110A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.747A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.151A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 733 through 734 removed outlier: 4.499A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.944A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 28 through 31 removed outlier: 3.701A pdb=" N ILE C 203 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.011A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN C 164 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER C 162 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 84 through 85 removed outlier: 3.503A pdb=" N VAL C 120 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.693A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN C 613 " --> pdb=" O GLY C 594 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER C 596 " --> pdb=" O LEU C 611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU C 611 " --> pdb=" O SER C 596 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.547A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER C 399 " --> pdb=" O ASN C 354 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AE4, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.694A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 655 through 660 removed outlier: 4.609A pdb=" N THR C 696 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN C 658 " --> pdb=" O THR C 696 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 711 through 728 removed outlier: 7.150A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N THR C 724 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU C1063 " --> pdb=" O THR C 724 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE C 726 " --> pdb=" O VAL C1061 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL C1061 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLY C1059 " --> pdb=" O PRO C 728 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.945A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'H' and resid 58 through 60 Processing sheet with id=AF3, first strand: chain 'L' and resid 4 through 7 removed outlier: 6.539A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.696A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.652A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AF6, first strand: chain 'I' and resid 58 through 60 Processing sheet with id=AF7, first strand: chain 'M' and resid 4 through 7 removed outlier: 6.540A pdb=" N THR M 69 " --> pdb=" O ALA M 25 " (cutoff:3.500A) removed outlier: 10.697A pdb=" N GLN M 27 " --> pdb=" O SER M 67 " (cutoff:3.500A) removed outlier: 10.098A pdb=" N SER M 67 " --> pdb=" O GLN M 27 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N ILE M 29 " --> pdb=" O SER M 65 " (cutoff:3.500A) removed outlier: 11.484A pdb=" N SER M 65 " --> pdb=" O ILE M 29 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 10 through 12 removed outlier: 6.652A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AG1, first strand: chain 'J' and resid 58 through 60 Processing sheet with id=AG2, first strand: chain 'N' and resid 4 through 7 removed outlier: 6.539A pdb=" N THR N 69 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 10.696A pdb=" N GLN N 27 " --> pdb=" O SER N 67 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N SER N 67 " --> pdb=" O GLN N 27 " (cutoff:3.500A) removed outlier: 11.754A pdb=" N ILE N 29 " --> pdb=" O SER N 65 " (cutoff:3.500A) removed outlier: 11.485A pdb=" N SER N 65 " --> pdb=" O ILE N 29 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.652A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) 1106 hydrogen bonds defined for protein. 2940 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: 15.86 Time building geometry restraints manager: 13.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 4888 1.28 - 1.42: 8248 1.42 - 1.55: 17904 1.55 - 1.68: 13 1.68 - 1.81: 177 Bond restraints: 31230 Sorted by residual: bond pdb=" C GLY B 857 " pdb=" O GLY B 857 " ideal model delta sigma weight residual 1.237 1.153 0.084 1.31e-02 5.83e+03 4.10e+01 bond pdb=" CA LEU B 858 " pdb=" C LEU B 858 " ideal model delta sigma weight residual 1.523 1.444 0.080 1.34e-02 5.57e+03 3.54e+01 bond pdb=" C LEU B 858 " pdb=" O LEU B 858 " ideal model delta sigma weight residual 1.235 1.161 0.074 1.26e-02 6.30e+03 3.47e+01 bond pdb=" C LEU B 858 " pdb=" N THR B 859 " ideal model delta sigma weight residual 1.332 1.267 0.066 1.40e-02 5.10e+03 2.21e+01 bond pdb=" N PRO B 561 " pdb=" CD PRO B 561 " ideal model delta sigma weight residual 1.473 1.538 -0.065 1.40e-02 5.10e+03 2.18e+01 ... (remaining 31225 not shown) Histogram of bond angle deviations from ideal: 100.10 - 107.82: 1559 107.82 - 115.54: 18448 115.54 - 123.25: 20703 123.25 - 130.97: 1649 130.97 - 138.69: 97 Bond angle restraints: 42456 Sorted by residual: angle pdb=" N THR C 588 " pdb=" CA THR C 588 " pdb=" C THR C 588 " ideal model delta sigma weight residual 110.40 100.10 10.30 1.31e+00 5.83e-01 6.18e+01 angle pdb=" C THR C 588 " pdb=" N PRO C 589 " pdb=" CA PRO C 589 " ideal model delta sigma weight residual 120.66 113.87 6.79 1.09e+00 8.42e-01 3.88e+01 angle pdb=" N THR B 588 " pdb=" CA THR B 588 " pdb=" C THR B 588 " ideal model delta sigma weight residual 110.39 103.14 7.25 1.30e+00 5.92e-01 3.11e+01 angle pdb=" N ASN M 53 " pdb=" CA ASN M 53 " pdb=" C ASN M 53 " ideal model delta sigma weight residual 107.98 118.45 -10.47 1.88e+00 2.83e-01 3.10e+01 angle pdb=" N ASN N 53 " pdb=" CA ASN N 53 " pdb=" C ASN N 53 " ideal model delta sigma weight residual 107.98 118.44 -10.46 1.88e+00 2.83e-01 3.09e+01 ... (remaining 42451 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 16272 17.93 - 35.86: 1285 35.86 - 53.79: 268 53.79 - 71.72: 71 71.72 - 89.65: 29 Dihedral angle restraints: 17925 sinusoidal: 7014 harmonic: 10911 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 157.32 -64.32 1 1.00e+01 1.00e-02 5.44e+01 dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 157.31 -64.31 1 1.00e+01 1.00e-02 5.44e+01 dihedral pdb=" CB CYS C 480 " pdb=" SG CYS C 480 " pdb=" SG CYS C 488 " pdb=" CB CYS C 488 " ideal model delta sinusoidal sigma weight residual 93.00 157.29 -64.29 1 1.00e+01 1.00e-02 5.44e+01 ... (remaining 17922 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.233: 4913 0.233 - 0.466: 20 0.466 - 0.699: 4 0.699 - 0.932: 0 0.932 - 1.164: 4 Chirality restraints: 4941 Sorted by residual: chirality pdb=" C1 NAG A1410 " pdb=" O4 NAG A1409 " pdb=" C2 NAG A1410 " pdb=" O5 NAG A1410 " both_signs ideal model delta sigma weight residual False -2.40 -3.09 0.69 2.00e-02 2.50e+03 1.19e+03 chirality pdb=" C1 NAG B1410 " pdb=" O4 NAG B1409 " pdb=" C2 NAG B1410 " pdb=" O5 NAG B1410 " both_signs ideal model delta sigma weight residual False -2.40 -3.09 0.69 2.00e-02 2.50e+03 1.18e+03 chirality pdb=" C1 NAG C1410 " pdb=" O4 NAG C1409 " pdb=" C2 NAG C1410 " pdb=" O5 NAG C1410 " both_signs ideal model delta sigma weight residual False -2.40 -3.08 0.68 2.00e-02 2.50e+03 1.17e+03 ... (remaining 4938 not shown) Planarity restraints: 5436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 603 " -0.061 2.00e-02 2.50e+03 8.55e-02 9.14e+01 pdb=" CG ASN A 603 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN A 603 " -0.020 2.00e-02 2.50e+03 pdb=" ND2 ASN A 603 " 0.151 2.00e-02 2.50e+03 pdb=" C1 NAG A1405 " -0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.073 2.00e-02 2.50e+03 8.05e-02 8.11e+01 pdb=" CG ASN C 331 " -0.028 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.016 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.128 2.00e-02 2.50e+03 pdb=" C1 NAG Y 1 " 0.099 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 331 " -0.051 2.00e-02 2.50e+03 6.82e-02 5.81e+01 pdb=" CG ASN B 331 " 0.025 2.00e-02 2.50e+03 pdb=" OD1 ASN B 331 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN B 331 " 0.117 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " -0.078 2.00e-02 2.50e+03 ... (remaining 5433 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 194 2.50 - 3.10: 21461 3.10 - 3.70: 42262 3.70 - 4.30: 63610 4.30 - 4.90: 107130 Nonbonded interactions: 234657 Sorted by model distance: nonbonded pdb=" O SER C 530 " pdb=" OG1 THR C 531 " model vdw 1.900 2.440 nonbonded pdb=" O GLN B 690 " pdb=" OG SER B 691 " model vdw 1.938 2.440 nonbonded pdb=" O PRO B 527 " pdb=" NZ LYS B 528 " model vdw 1.951 2.520 nonbonded pdb=" O PRO A 322 " pdb=" OG1 THR A 323 " model vdw 1.971 2.440 nonbonded pdb=" OD1 ASN C 532 " pdb=" N LEU C 533 " model vdw 1.991 2.520 ... (remaining 234652 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'Q' selection = chain 'X' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 8.900 Check model and map are aligned: 0.500 Set scattering table: 0.340 Process input model: 85.270 Find NCS groups from input model: 1.900 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 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 : 0.009 0.084 31230 Z= 0.616 Angle : 1.048 13.688 42456 Z= 0.617 Chirality : 0.075 1.164 4941 Planarity : 0.007 0.107 5388 Dihedral : 14.019 89.655 10803 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 1.87 % Allowed : 7.34 % Favored : 90.79 % Rotamer: Outliers : 3.06 % Allowed : 6.74 % Favored : 90.20 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 3.08 % 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: -3.05 (0.12), residues: 3693 helix: -1.15 (0.17), residues: 643 sheet: -1.54 (0.15), residues: 1067 loop : -2.66 (0.11), residues: 1983 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 770 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 670 time to evaluate : 3.427 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: 100 outliers final: 41 residues processed: 759 average time/residue: 0.4378 time to fit residues: 523.4827 Evaluate side-chains 385 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 344 time to evaluate : 3.752 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 1 residues processed: 41 average time/residue: 0.3211 time to fit residues: 28.8247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 314 optimal weight: 3.9990 chunk 281 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 chunk 96 optimal weight: 0.8980 chunk 190 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 291 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 337 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN A 164 ASN A 173 GLN A 207 HIS A 422 ASN A 450 ASN A 607 GLN A 613 GLN A 690 GLN A 907 ASN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1106 GLN B 87 ASN B 121 ASN B 164 ASN B 414 GLN B 422 ASN B 450 ASN B 607 GLN B 613 GLN B 774 GLN B 914 ASN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN C 121 ASN C 164 ASN C 422 ASN C 450 ASN C 607 GLN C 613 GLN C 955 ASN H 35 HIS ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 35 HIS I 82 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 ASN N 53 ASN N 79 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 31230 Z= 0.256 Angle : 0.714 9.745 42456 Z= 0.367 Chirality : 0.048 0.375 4941 Planarity : 0.006 0.109 5388 Dihedral : 5.377 29.133 4053 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.07 % Favored : 93.61 % Rotamer: Outliers : 2.70 % Allowed : 13.20 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -2.17 (0.12), residues: 3693 helix: 0.24 (0.20), residues: 660 sheet: -1.13 (0.15), residues: 1054 loop : -2.26 (0.12), residues: 1979 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 384 time to evaluate : 3.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 32 residues processed: 452 average time/residue: 0.4024 time to fit residues: 298.4807 Evaluate side-chains 340 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 308 time to evaluate : 3.665 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 32 outliers final: 1 residues processed: 32 average time/residue: 0.2865 time to fit residues: 22.1794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 187 optimal weight: 4.9990 chunk 104 optimal weight: 10.0000 chunk 281 optimal weight: 0.0060 chunk 230 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 338 optimal weight: 7.9990 chunk 365 optimal weight: 20.0000 chunk 301 optimal weight: 0.5980 chunk 335 optimal weight: 8.9990 chunk 115 optimal weight: 0.2980 chunk 271 optimal weight: 1.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 913 GLN ** B1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 GLN L 6 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 GLN M 79 GLN J 57 ASN N 6 GLN ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6996 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 31230 Z= 0.207 Angle : 0.628 8.535 42456 Z= 0.318 Chirality : 0.046 0.275 4941 Planarity : 0.004 0.055 5388 Dihedral : 4.914 28.073 4053 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.90 % Favored : 93.88 % Rotamer: Outliers : 1.78 % Allowed : 14.31 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -1.69 (0.13), residues: 3693 helix: 0.74 (0.20), residues: 657 sheet: -0.79 (0.16), residues: 995 loop : -1.99 (0.12), residues: 2041 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 327 time to evaluate : 3.251 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: 58 outliers final: 18 residues processed: 372 average time/residue: 0.4254 time to fit residues: 261.1906 Evaluate side-chains 309 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 291 time to evaluate : 3.378 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2825 time to fit residues: 14.5435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 334 optimal weight: 4.9990 chunk 254 optimal weight: 0.8980 chunk 175 optimal weight: 5.9990 chunk 37 optimal weight: 40.0000 chunk 161 optimal weight: 7.9990 chunk 227 optimal weight: 4.9990 chunk 339 optimal weight: 9.9990 chunk 359 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 321 optimal weight: 9.9990 chunk 96 optimal weight: 0.0020 overall best weight: 2.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 121 ASN B 914 ASN H 3 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN J 57 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.4309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 31230 Z= 0.325 Angle : 0.665 8.695 42456 Z= 0.337 Chirality : 0.048 0.238 4941 Planarity : 0.005 0.069 5388 Dihedral : 4.883 27.729 4053 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.36 % Favored : 93.45 % Rotamer: Outliers : 2.14 % Allowed : 14.55 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -1.48 (0.13), residues: 3693 helix: 0.79 (0.21), residues: 649 sheet: -0.64 (0.16), residues: 993 loop : -1.81 (0.12), residues: 2051 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 313 time to evaluate : 3.376 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: 70 outliers final: 31 residues processed: 364 average time/residue: 0.4246 time to fit residues: 253.6366 Evaluate side-chains 311 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 280 time to evaluate : 3.451 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.2931 time to fit residues: 22.0579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 299 optimal weight: 1.9990 chunk 204 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 267 optimal weight: 0.6980 chunk 148 optimal weight: 0.9980 chunk 306 optimal weight: 7.9990 chunk 248 optimal weight: 50.0000 chunk 0 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 322 optimal weight: 20.0000 chunk 90 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN B 115 GLN C 644 GLN C 755 GLN H 30 ASN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 30 ASN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN J 57 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.4615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31230 Z= 0.218 Angle : 0.594 10.834 42456 Z= 0.300 Chirality : 0.045 0.233 4941 Planarity : 0.004 0.049 5388 Dihedral : 4.642 33.628 4053 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.63 % Favored : 94.23 % Rotamer: Outliers : 1.10 % Allowed : 16.08 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -1.20 (0.13), residues: 3693 helix: 0.96 (0.21), residues: 655 sheet: -0.48 (0.16), residues: 1040 loop : -1.61 (0.13), residues: 1998 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 304 time to evaluate : 3.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 13 residues processed: 333 average time/residue: 0.4320 time to fit residues: 235.7307 Evaluate side-chains 290 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 277 time to evaluate : 3.259 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.3088 time to fit residues: 11.7783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 120 optimal weight: 2.9990 chunk 323 optimal weight: 20.0000 chunk 71 optimal weight: 0.7980 chunk 211 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 359 optimal weight: 8.9990 chunk 298 optimal weight: 0.9990 chunk 166 optimal weight: 6.9990 chunk 29 optimal weight: 40.0000 chunk 119 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 755 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN M 79 GLN J 57 ASN ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 31230 Z= 0.265 Angle : 0.621 13.133 42456 Z= 0.311 Chirality : 0.046 0.239 4941 Planarity : 0.004 0.049 5388 Dihedral : 4.591 32.845 4053 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.12 % Favored : 93.74 % Rotamer: Outliers : 1.10 % Allowed : 16.85 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -1.12 (0.13), residues: 3693 helix: 0.96 (0.21), residues: 662 sheet: -0.45 (0.16), residues: 1047 loop : -1.53 (0.13), residues: 1984 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 299 time to evaluate : 3.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 18 residues processed: 328 average time/residue: 0.4178 time to fit residues: 223.4132 Evaluate side-chains 293 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 275 time to evaluate : 3.243 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.2646 time to fit residues: 13.5800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 347 optimal weight: 20.0000 chunk 40 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 302 optimal weight: 0.5980 chunk 200 optimal weight: 0.3980 chunk 358 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 218 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 755 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN M 34 ASN J 57 ASN J 98 ASN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 31230 Z= 0.224 Angle : 0.591 12.127 42456 Z= 0.296 Chirality : 0.045 0.264 4941 Planarity : 0.004 0.049 5388 Dihedral : 4.492 32.868 4053 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.85 % Favored : 94.02 % Rotamer: Outliers : 0.74 % Allowed : 17.49 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -1.01 (0.14), residues: 3693 helix: 1.09 (0.21), residues: 663 sheet: -0.39 (0.15), residues: 1083 loop : -1.48 (0.13), residues: 1947 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 287 time to evaluate : 3.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 10 residues processed: 302 average time/residue: 0.4298 time to fit residues: 212.5893 Evaluate side-chains 279 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 269 time to evaluate : 3.321 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.2837 time to fit residues: 10.0063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 221 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 70 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 244 optimal weight: 20.0000 chunk 177 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 281 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 914 ASN C 755 GLN C1106 GLN ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN M 34 ASN J 30 ASN J 57 ASN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 31230 Z= 0.329 Angle : 0.649 14.374 42456 Z= 0.326 Chirality : 0.048 0.509 4941 Planarity : 0.004 0.050 5388 Dihedral : 4.644 30.021 4053 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.77 % Favored : 93.10 % Rotamer: Outliers : 0.83 % Allowed : 17.89 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -1.05 (0.14), residues: 3693 helix: 1.04 (0.21), residues: 654 sheet: -0.42 (0.15), residues: 1081 loop : -1.49 (0.13), residues: 1958 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 278 time to evaluate : 3.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 11 residues processed: 299 average time/residue: 0.4268 time to fit residues: 207.9958 Evaluate side-chains 277 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 266 time to evaluate : 3.477 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.2762 time to fit residues: 10.6140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 326 optimal weight: 0.9990 chunk 343 optimal weight: 10.0000 chunk 313 optimal weight: 5.9990 chunk 334 optimal weight: 0.6980 chunk 201 optimal weight: 0.6980 chunk 145 optimal weight: 20.0000 chunk 262 optimal weight: 0.8980 chunk 102 optimal weight: 6.9990 chunk 301 optimal weight: 0.5980 chunk 316 optimal weight: 9.9990 chunk 332 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.5426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 31230 Z= 0.176 Angle : 0.585 13.191 42456 Z= 0.295 Chirality : 0.045 0.224 4941 Planarity : 0.004 0.049 5388 Dihedral : 4.458 31.629 4053 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.50 % Favored : 94.37 % Rotamer: Outliers : 0.18 % Allowed : 18.50 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: -0.84 (0.14), residues: 3693 helix: 1.32 (0.21), residues: 650 sheet: -0.26 (0.16), residues: 1065 loop : -1.40 (0.13), residues: 1978 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7386 Ramachandran restraints generated. 3693 Oldfield, 0 Emsley, 3693 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 286 time to evaluate : 3.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 289 average time/residue: 0.4269 time to fit residues: 200.3931 Evaluate side-chains 270 residues out of total 3264 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 266 time to evaluate : 3.185 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.2779 time to fit residues: 7.0095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 219 optimal weight: 0.8980 chunk 353 optimal weight: 7.9990 chunk 215 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 245 optimal weight: 0.0980 chunk 370 optimal weight: 6.9990 chunk 341 optimal weight: 0.5980 chunk 295 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 chunk 180 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.5546 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: