Starting phenix.real_space_refine on Wed Feb 21 07:38:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xic_33202/02_2024/7xic_33202.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xic_33202/02_2024/7xic_33202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xic_33202/02_2024/7xic_33202.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xic_33202/02_2024/7xic_33202.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xic_33202/02_2024/7xic_33202.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xic_33202/02_2024/7xic_33202.pdb" } resolution = 3.3 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= 0.009 sd= 0.085 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 19039 2.51 5 N 4908 2.21 5 O 5859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 357": "NH1" <-> "NH2" Residue "A ARG 408": "NH1" <-> "NH2" Residue "A GLU 471": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ARG 408": "NH1" <-> "NH2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "C ARG 357": "NH1" <-> "NH2" Residue "C ARG 408": "NH1" <-> "NH2" Residue "C GLU 471": "OE1" <-> "OE2" Residue "E GLU 1": "OE1" <-> "OE2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E GLU 46": "OE1" <-> "OE2" Residue "E GLU 89": "OE1" <-> "OE2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "F GLU 1": "OE1" <-> "OE2" Residue "F GLU 17": "OE1" <-> "OE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 70": "OE1" <-> "OE2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F GLU 106": "OE1" <-> "OE2" Residue "H GLU 1": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 89": "OE1" <-> "OE2" Residue "H GLU 129": "OE1" <-> "OE2" Residue "I GLU 1": "OE1" <-> "OE2" Residue "I GLU 17": "OE1" <-> "OE2" Residue "I GLU 70": "OE1" <-> "OE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I GLU 106": "OE1" <-> "OE2" Residue "K GLU 1": "OE1" <-> "OE2" Residue "K GLU 6": "OE1" <-> "OE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K GLU 89": "OE1" <-> "OE2" Residue "K GLU 129": "OE1" <-> "OE2" Residue "L GLU 1": "OE1" <-> "OE2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L GLU 70": "OE1" <-> "OE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L GLU 106": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 29941 Number of models: 1 Model: "" Number of chains: 31 Chain: "A" Number of atoms: 7848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 999, 7848 Classifications: {'peptide': 999} Link IDs: {'PTRANS': 54, 'TRANS': 944} Chain breaks: 9 Chain: "B" Number of atoms: 7842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7842 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "C" Number of atoms: 7842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 998, 7842 Classifications: {'peptide': 998} Link IDs: {'PTRANS': 54, 'TRANS': 943} Chain breaks: 9 Chain: "E" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 968 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "F" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 968 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "I" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 968 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 125} Chain: "L" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 4, 'TRANS': 100} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 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 dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Time building chain proxies: 16.18, per 1000 atoms: 0.54 Number of scatterers: 29941 At special positions: 0 Unit cell: (168.485, 160.876, 194.573, 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 5859 8.00 N 4908 7.00 C 19039 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.19 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=1.97 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.12 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.00 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.15 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.07 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.02 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.15 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.15 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.12 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.18 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.07 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.14 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.10 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.12 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.00 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.14 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.07 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.20 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=1.99 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.17 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=2.09 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.18 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.12 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.00 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.09 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.07 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.01 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.06 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.05 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.08 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.02 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.04 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.20 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 102 " - pdb=" SG CYS E 106 " distance=2.09 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 102 " - pdb=" SG CYS H 106 " distance=2.09 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Simple disulfide: pdb=" SG CYS K 102 " - pdb=" SG CYS K 106 " distance=2.09 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 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 A1406 " - " NAG A1407 " " NAG B1406 " - " NAG B1407 " " NAG B1411 " - " NAG B1412 " " NAG C1406 " - " NAG C1407 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG J 1 " - " NAG J 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " NAG-ASN " NAG A1401 " - " ASN A 61 " " NAG A1402 " - " ASN A 122 " " NAG A1403 " - " ASN A 165 " " NAG A1404 " - " ASN A 234 " " NAG A1405 " - " ASN A 282 " " NAG A1406 " - " ASN A 343 " " NAG A1408 " - " ASN A 603 " " NAG A1409 " - " ASN A 616 " " NAG A1410 " - " ASN A 657 " " NAG A1411 " - " ASN A 709 " " NAG B1401 " - " ASN B 61 " " NAG B1402 " - " ASN B 122 " " NAG B1403 " - " ASN B 165 " " NAG B1404 " - " ASN B 234 " " NAG B1405 " - " ASN B 282 " " NAG B1406 " - " ASN B 343 " " NAG B1408 " - " ASN B 603 " " NAG B1409 " - " ASN B 616 " " NAG B1410 " - " ASN B 657 " " NAG B1411 " - " ASN B1074 " " NAG C1401 " - " ASN C 61 " " NAG C1402 " - " ASN C 122 " " NAG C1403 " - " ASN C 165 " " NAG C1404 " - " ASN C 234 " " NAG C1405 " - " ASN C 282 " " NAG C1406 " - " ASN C 343 " " NAG C1408 " - " ASN C 603 " " NAG C1409 " - " ASN C 616 " " NAG C1410 " - " ASN C 657 " " NAG D 1 " - " ASN A 331 " " NAG G 1 " - " ASN A 717 " " NAG J 1 " - " ASN A 801 " " NAG M 1 " - " ASN A1074 " " NAG N 1 " - " ASN A1098 " " NAG O 1 " - " ASN A1134 " " NAG P 1 " - " ASN B 331 " " NAG Q 1 " - " ASN B 709 " " NAG R 1 " - " ASN B 717 " " NAG S 1 " - " ASN B 801 " " NAG T 1 " - " ASN B1098 " " NAG U 1 " - " ASN B1134 " " NAG V 1 " - " ASN C 331 " " NAG W 1 " - " ASN C 709 " " NAG X 1 " - " ASN C 717 " " NAG Y 1 " - " ASN C 801 " " NAG Z 1 " - " ASN C1074 " " NAG a 1 " - " ASN C1098 " " NAG b 1 " - " ASN C1134 " Time building additional restraints: 12.71 Conformation dependent library (CDL) restraints added in 5.2 seconds 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6884 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 60 sheets defined 22.5% alpha, 33.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.73 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.689A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU A 368 " --> pdb=" O TYR A 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 364 through 368' Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.479A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.542A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.530A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.790A pdb=" N LYS A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLU A 773 " --> pdb=" O GLY A 769 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN A 774 " --> pdb=" O ILE A 770 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 811 through 815 Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 866 through 885 removed outlier: 3.701A pdb=" N THR A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 908 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.252A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 932 Processing helix chain 'A' and resid 933 through 940 Processing helix chain 'A' and resid 945 through 964 removed outlier: 3.761A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 968 removed outlier: 3.702A pdb=" N SER A 968 " --> pdb=" O GLN A 965 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 965 through 968' Processing helix chain 'A' and resid 976 through 981 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.757A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1146 removed outlier: 3.982A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 349 through 353 Processing helix chain 'B' and resid 364 through 368 removed outlier: 3.686A pdb=" N VAL B 367 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 368 " --> pdb=" O TYR B 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 364 through 368' Processing helix chain 'B' and resid 383 through 388 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.479A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.542A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 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: 3.985A 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: 3.589A pdb=" N LEU B 821 " --> pdb=" O PRO B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 removed outlier: 3.514A pdb=" N THR B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 890 removed outlier: 3.576A 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: 4.240A 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: 3.595A 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: 3.678A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) removed outlier: 3.536A 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 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 349 through 353 Processing helix chain 'C' and resid 364 through 368 removed outlier: 3.688A pdb=" N VAL C 367 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU C 368 " --> pdb=" O TYR C 365 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 364 through 368' Processing helix chain 'C' and resid 383 through 388 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.478A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.542A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 753 Processing helix chain 'C' and resid 754 through 756 No H-bonds generated for 'chain 'C' and resid 754 through 756' Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.612A pdb=" N ILE C 770 " --> pdb=" O ALA C 766 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU C 773 " --> pdb=" O GLY C 769 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN C 774 " --> pdb=" O ILE C 770 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS C 776 " --> pdb=" O VAL C 772 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 removed outlier: 3.655A pdb=" N LEU C 821 " --> pdb=" O PRO C 817 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL C 826 " --> pdb=" O LEU C 822 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 884 Processing helix chain 'C' and resid 897 through 908 Processing helix chain 'C' and resid 913 through 918 Processing helix chain 'C' and resid 919 through 933 Processing helix chain 'C' and resid 933 through 939 Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.322A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 981 removed outlier: 3.810A pdb=" N PHE C 981 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 1033 removed outlier: 3.931A pdb=" N VAL C 991 " --> pdb=" O PRO C 987 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 1140 through 1146 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'F' and resid 50 through 52 No H-bonds generated for 'chain 'F' and resid 50 through 52' Processing helix chain 'F' and resid 79 through 83 removed outlier: 3.895A pdb=" N PHE F 83 " --> pdb=" O SER F 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'I' and resid 50 through 52 No H-bonds generated for 'chain 'I' and resid 50 through 52' Processing helix chain 'I' and resid 79 through 83 removed outlier: 3.896A pdb=" N PHE I 83 " --> pdb=" O SER I 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 87 through 91 Processing helix chain 'L' and resid 50 through 52 No H-bonds generated for 'chain 'L' and resid 50 through 52' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.896A pdb=" N PHE L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.514A pdb=" N THR A 63 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 55 removed outlier: 7.395A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.326A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ASN A 121 " --> pdb=" O ARG A 102 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N ILE A 128 " --> pdb=" O PHE A 168 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N PHE A 168 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL A 130 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N CYS A 166 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN A 134 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N SER A 162 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.306A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU A 224 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 319 removed outlier: 5.469A pdb=" N ILE A 312 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N THR A 599 " --> pdb=" O ILE A 312 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N GLN A 314 " --> pdb=" O VAL A 597 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 597 " --> pdb=" O GLN A 314 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY A 594 " --> pdb=" O GLN A 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 323 through 328 removed outlier: 5.676A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.962A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.292A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.685A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 702 through 703 Processing sheet with id=AB2, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.753A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLY A1059 " --> pdb=" O ALA A1056 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.753A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.485A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 788 through 790 removed outlier: 5.768A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.851A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 28 through 30 removed outlier: 3.589A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 93 " --> pdb=" O TYR B 266 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N PHE B 201 " --> pdb=" O ASP B 228 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ASP B 228 " --> pdb=" O PHE B 201 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 49 through 55 removed outlier: 7.471A pdb=" N THR B 274 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ASP B 290 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N LEU B 276 " --> pdb=" O ALA B 288 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ALA B 288 " --> pdb=" O LEU B 276 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS B 278 " --> pdb=" O THR B 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.512A pdb=" N ILE B 105 " --> pdb=" O GLN B 239 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N ASN B 121 " --> pdb=" O ARG B 102 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N CYS B 131 " --> pdb=" O SER B 116 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL B 120 " --> pdb=" O VAL B 127 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE B 128 " --> pdb=" O PHE B 168 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N PHE B 168 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N VAL B 130 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N CYS B 166 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN B 134 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER B 162 " --> pdb=" O GLN B 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 311 through 319 removed outlier: 5.696A pdb=" N ILE B 312 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N THR B 599 " --> pdb=" O ILE B 312 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N GLN B 314 " --> pdb=" O VAL B 597 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL B 597 " --> pdb=" O GLN B 314 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER B 316 " --> pdb=" O VAL B 595 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLN B 613 " --> pdb=" O GLY B 594 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N SER B 596 " --> pdb=" O LEU B 611 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU B 611 " --> pdb=" O SER B 596 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 323 through 328 removed outlier: 5.857A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.815A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.962A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.239A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 660 removed outlier: 5.577A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 8.443A pdb=" N VAL B 656 " --> pdb=" O THR B 696 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 702 through 704 removed outlier: 3.546A pdb=" N ASN B 703 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LYS C 790 " --> pdb=" O ASN B 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.152A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.050A 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: 6.994A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 711 through 728 removed outlier: 7.152A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 7.050A 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: 6.994A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.973A 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=AD1, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.499A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.943A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 28 through 30 removed outlier: 3.685A pdb=" N THR C 63 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 267 " --> pdb=" O THR C 63 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 49 through 55 removed outlier: 7.498A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 84 through 85 removed outlier: 6.924A pdb=" N ARG C 237 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 4.845A pdb=" N PHE C 106 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN C 239 " --> pdb=" O TRP C 104 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N TRP C 104 " --> pdb=" O GLN C 239 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU C 241 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL C 130 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU C 132 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N ASN C 165 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 8.339A pdb=" N GLN C 134 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N ALA C 163 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 90 through 92 removed outlier: 3.738A pdb=" N GLU C 224 " --> pdb=" O SER C 205 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 311 through 319 removed outlier: 5.478A pdb=" N ILE C 312 " --> pdb=" O THR C 599 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N THR C 599 " --> pdb=" O ILE C 312 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N GLN C 314 " --> pdb=" O VAL C 597 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL C 597 " --> pdb=" O GLN C 314 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 323 through 328 removed outlier: 5.456A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.962A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AE2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.307A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.705A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.892A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.892A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 733 through 735 removed outlier: 4.301A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1120 through 1122 Processing sheet with id=AE7, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.286A pdb=" N GLY E 33 " --> pdb=" O VAL E 99 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.629A pdb=" N TYR E 117 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 4 through 7 removed outlier: 3.551A pdb=" N GLU F 70 " --> pdb=" O SER F 67 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'F' and resid 10 through 13 removed outlier: 6.528A pdb=" N LEU F 33 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TYR F 49 " --> pdb=" O LEU F 33 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 10 through 13 Processing sheet with id=AF4, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF5, first strand: chain 'H' and resid 10 through 12 removed outlier: 4.287A pdb=" N GLY H 33 " --> pdb=" O VAL H 99 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLY H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.630A pdb=" N TYR H 117 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.550A pdb=" N GLU I 70 " --> pdb=" O SER I 67 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.528A pdb=" N LEU I 33 " --> pdb=" O TYR I 49 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR I 49 " --> pdb=" O LEU I 33 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 10 through 13 Processing sheet with id=AG1, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AG2, first strand: chain 'K' and resid 10 through 12 removed outlier: 4.286A pdb=" N GLY K 33 " --> pdb=" O VAL K 99 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N MET K 34 " --> pdb=" O GLY K 50 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLY K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.630A pdb=" N TYR K 117 " --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.550A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.528A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 10 through 13 1181 hydrogen bonds defined for protein. 3117 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.92 Time building geometry restraints manager: 13.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6644 1.33 - 1.45: 8265 1.45 - 1.58: 15539 1.58 - 1.71: 0 1.71 - 1.84: 171 Bond restraints: 30619 Sorted by residual: bond pdb=" CA SER A 698 " pdb=" C SER A 698 " ideal model delta sigma weight residual 1.522 1.442 0.080 1.20e-02 6.94e+03 4.40e+01 bond pdb=" C THR C 208 " pdb=" N PRO C 209 " ideal model delta sigma weight residual 1.329 1.387 -0.058 1.20e-02 6.94e+03 2.36e+01 bond pdb=" C THR A 208 " pdb=" N PRO A 209 " ideal model delta sigma weight residual 1.329 1.386 -0.057 1.25e-02 6.40e+03 2.07e+01 bond pdb=" C THR B 208 " pdb=" N PRO B 209 " ideal model delta sigma weight residual 1.329 1.386 -0.057 1.25e-02 6.40e+03 2.05e+01 bond pdb=" N PRO B 521 " pdb=" CD PRO B 521 " ideal model delta sigma weight residual 1.473 1.534 -0.061 1.40e-02 5.10e+03 1.87e+01 ... (remaining 30614 not shown) Histogram of bond angle deviations from ideal: 99.58 - 107.30: 1226 107.30 - 115.01: 18022 115.01 - 122.73: 18506 122.73 - 130.44: 3758 130.44 - 138.16: 108 Bond angle restraints: 41620 Sorted by residual: angle pdb=" N PHE A 375 " pdb=" CA PHE A 375 " pdb=" C PHE A 375 " ideal model delta sigma weight residual 110.28 123.15 -12.87 1.48e+00 4.57e-01 7.56e+01 angle pdb=" N PHE C 375 " pdb=" CA PHE C 375 " pdb=" C PHE C 375 " ideal model delta sigma weight residual 110.28 123.14 -12.86 1.48e+00 4.57e-01 7.55e+01 angle pdb=" N PHE B 375 " pdb=" CA PHE B 375 " pdb=" C PHE B 375 " ideal model delta sigma weight residual 110.28 123.12 -12.84 1.48e+00 4.57e-01 7.53e+01 angle pdb=" N ILE A 794 " pdb=" CA ILE A 794 " pdb=" C ILE A 794 " ideal model delta sigma weight residual 110.05 103.16 6.89 1.09e+00 8.42e-01 3.99e+01 angle pdb=" C THR C 208 " pdb=" N PRO C 209 " pdb=" CA PRO C 209 " ideal model delta sigma weight residual 120.31 114.31 6.00 9.80e-01 1.04e+00 3.75e+01 ... (remaining 41615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.67: 18164 17.67 - 35.34: 704 35.34 - 53.02: 175 53.02 - 70.69: 61 70.69 - 88.36: 28 Dihedral angle restraints: 19132 sinusoidal: 8398 harmonic: 10734 Sorted by residual: dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -16.74 -69.26 1 1.00e+01 1.00e-02 6.20e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -23.70 -62.30 1 1.00e+01 1.00e-02 5.14e+01 dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -132.52 46.52 1 1.00e+01 1.00e-02 2.99e+01 ... (remaining 19129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.330: 4837 0.330 - 0.660: 6 0.660 - 0.990: 6 0.990 - 1.321: 3 1.321 - 1.651: 1 Chirality restraints: 4853 Sorted by residual: chirality pdb=" C1 NAG C1407 " pdb=" O4 NAG C1406 " pdb=" C2 NAG C1407 " pdb=" O5 NAG C1407 " both_signs ideal model delta sigma weight residual False -2.40 -1.40 -1.00 2.00e-02 2.50e+03 2.52e+03 chirality pdb=" C1 NAG A1407 " pdb=" O4 NAG A1406 " pdb=" C2 NAG A1407 " pdb=" O5 NAG A1407 " both_signs ideal model delta sigma weight residual False -2.40 -1.40 -1.00 2.00e-02 2.50e+03 2.52e+03 chirality pdb=" C1 NAG B1407 " pdb=" O4 NAG B1406 " pdb=" C2 NAG B1407 " pdb=" O5 NAG B1407 " both_signs ideal model delta sigma weight residual False -2.40 -1.40 -1.00 2.00e-02 2.50e+03 2.50e+03 ... (remaining 4850 not shown) Planarity restraints: 5337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 331 " 0.252 2.00e-02 2.50e+03 2.98e-01 1.11e+03 pdb=" CG ASN C 331 " -0.104 2.00e-02 2.50e+03 pdb=" OD1 ASN C 331 " -0.041 2.00e-02 2.50e+03 pdb=" ND2 ASN C 331 " -0.480 2.00e-02 2.50e+03 pdb=" C1 NAG V 1 " 0.372 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " 0.197 2.00e-02 2.50e+03 2.43e-01 7.41e+02 pdb=" CG ASN A 343 " -0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " -0.415 2.00e-02 2.50e+03 pdb=" C1 NAG A1406 " 0.281 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 343 " 0.197 2.00e-02 2.50e+03 2.43e-01 7.40e+02 pdb=" CG ASN C 343 " -0.077 2.00e-02 2.50e+03 pdb=" OD1 ASN C 343 " 0.014 2.00e-02 2.50e+03 pdb=" ND2 ASN C 343 " -0.415 2.00e-02 2.50e+03 pdb=" C1 NAG C1406 " 0.281 2.00e-02 2.50e+03 ... (remaining 5334 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 102 2.53 - 3.12: 22539 3.12 - 3.71: 42510 3.71 - 4.31: 65103 4.31 - 4.90: 105803 Nonbonded interactions: 236057 Sorted by model distance: nonbonded pdb=" O ARG A 328 " pdb=" CD1 PHE A 329 " model vdw 1.933 3.340 nonbonded pdb=" O ASN B 334 " pdb=" O VAL B 362 " model vdw 2.210 3.040 nonbonded pdb=" CG PRO B 521 " pdb=" OH TYR C 200 " model vdw 2.233 3.440 nonbonded pdb=" O GLY H 104 " pdb=" N CYS H 106 " model vdw 2.238 2.520 nonbonded pdb=" O GLY K 104 " pdb=" N CYS K 106 " model vdw 2.238 2.520 ... (remaining 236052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 939 or resid 944 through 1146 or resid 1401 thr \ ough 1410)) selection = (chain 'B' and (resid 27 through 1146 or resid 1401 through 1410)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' } ncs_group { reference = chain 'E' selection = chain 'H' selection = chain 'K' } ncs_group { reference = chain 'F' selection = chain 'I' selection = chain 'L' } 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: 1.110 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: 0.040 Extract box with map and model: 7.040 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 81.200 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 96.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 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 0.104 30619 Z= 0.615 Angle : 1.139 13.158 41620 Z= 0.705 Chirality : 0.080 1.651 4853 Planarity : 0.007 0.098 5289 Dihedral : 10.860 88.361 12104 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 1.84 % Allowed : 5.64 % Favored : 92.52 % Rotamer: Outliers : 1.40 % Allowed : 2.46 % Favored : 96.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: -2.01 (0.13), residues: 3634 helix: -1.27 (0.17), residues: 676 sheet: -0.43 (0.15), residues: 966 loop : -1.85 (0.13), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.130 0.012 TRP H 53 HIS 0.006 0.001 HIS E 95 PHE 0.034 0.002 PHE K 29 TYR 0.070 0.004 TYR L 36 ARG 0.007 0.001 ARG L 54 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 452 time to evaluate : 3.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ILE cc_start: 0.7706 (mm) cc_final: 0.7504 (tp) REVERT: B 408 ARG cc_start: 0.1885 (OUTLIER) cc_final: 0.1149 (ptm160) REVERT: B 569 ILE cc_start: 0.8825 (tt) cc_final: 0.8520 (tt) outliers start: 45 outliers final: 13 residues processed: 497 average time/residue: 0.4613 time to fit residues: 361.7615 Evaluate side-chains 220 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 206 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 529 LYS Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 525 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 102 CYS Chi-restraints excluded: chain H residue 99 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 306 optimal weight: 7.9990 chunk 275 optimal weight: 0.7980 chunk 152 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 284 optimal weight: 0.9980 chunk 110 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 211 optimal weight: 1.9990 chunk 329 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 207 HIS A 239 GLN A 388 ASN A 544 ASN B 52 GLN B 239 GLN B 388 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 580 GLN B 613 GLN B 675 GLN B 914 ASN B 935 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 388 ASN C 690 GLN C 907 ASN C 913 GLN C 992 GLN C1010 GLN K 82 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6544 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.110 30619 Z= 0.248 Angle : 0.729 15.078 41620 Z= 0.366 Chirality : 0.049 0.424 4853 Planarity : 0.005 0.068 5289 Dihedral : 5.934 59.383 5512 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.95 % Favored : 94.80 % Rotamer: Outliers : 2.43 % Allowed : 6.14 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: -1.14 (0.13), residues: 3634 helix: 0.35 (0.20), residues: 664 sheet: -0.35 (0.15), residues: 971 loop : -1.35 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 53 HIS 0.005 0.001 HIS A1064 PHE 0.032 0.002 PHE B 823 TYR 0.026 0.002 TYR B 369 ARG 0.012 0.001 ARG C 995 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 232 time to evaluate : 3.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 HIS cc_start: 0.6619 (OUTLIER) cc_final: 0.5984 (m90) REVERT: B 408 ARG cc_start: 0.2042 (OUTLIER) cc_final: 0.1156 (ptm160) REVERT: C 982 SER cc_start: 0.3657 (OUTLIER) cc_final: 0.3264 (p) REVERT: K 105 ASP cc_start: -0.4268 (OUTLIER) cc_final: -0.4638 (t0) REVERT: L 33 LEU cc_start: 0.4736 (tt) cc_final: 0.4510 (tp) REVERT: L 98 THR cc_start: 0.5610 (m) cc_final: 0.4781 (p) outliers start: 78 outliers final: 42 residues processed: 302 average time/residue: 0.3946 time to fit residues: 195.2913 Evaluate side-chains 210 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 164 time to evaluate : 3.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 HIS Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 207 HIS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 313 TYR Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 408 ARG Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 693 ILE Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1116 THR Chi-restraints excluded: chain B residue 1128 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 265 TYR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 738 CYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 982 SER Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 105 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 183 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 274 optimal weight: 2.9990 chunk 224 optimal weight: 30.0000 chunk 90 optimal weight: 1.9990 chunk 330 optimal weight: 40.0000 chunk 356 optimal weight: 10.0000 chunk 294 optimal weight: 5.9990 chunk 327 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 264 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** A 762 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 30 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 762 GLN ** C 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.149 30619 Z= 0.460 Angle : 0.796 18.096 41620 Z= 0.406 Chirality : 0.051 0.364 4853 Planarity : 0.006 0.068 5289 Dihedral : 6.152 50.837 5499 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.38 % Favored : 93.37 % Rotamer: Outliers : 2.71 % Allowed : 7.73 % Favored : 89.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: -1.16 (0.13), residues: 3634 helix: 0.34 (0.20), residues: 664 sheet: -0.40 (0.16), residues: 929 loop : -1.35 (0.13), residues: 2041 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B1102 HIS 0.037 0.002 HIS A 207 PHE 0.037 0.003 PHE A 855 TYR 0.040 0.002 TYR B 674 ARG 0.012 0.001 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 182 time to evaluate : 3.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 PHE cc_start: 0.3920 (OUTLIER) cc_final: 0.3554 (m-80) REVERT: A 1002 GLN cc_start: 0.7022 (mm110) cc_final: 0.6752 (mm-40) REVERT: B 533 LEU cc_start: 0.4367 (mt) cc_final: 0.3703 (tt) REVERT: C 200 TYR cc_start: 0.6059 (OUTLIER) cc_final: 0.5738 (m-10) outliers start: 87 outliers final: 58 residues processed: 263 average time/residue: 0.3883 time to fit residues: 171.5201 Evaluate side-chains 196 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 136 time to evaluate : 3.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 620 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 282 ASN Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 200 TYR Chi-restraints excluded: chain C residue 282 ASN Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 391 CYS Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 602 THR Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 690 GLN Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 102 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 326 optimal weight: 50.0000 chunk 248 optimal weight: 0.9990 chunk 171 optimal weight: 0.9990 chunk 36 optimal weight: 30.0000 chunk 157 optimal weight: 4.9990 chunk 221 optimal weight: 9.9990 chunk 331 optimal weight: 40.0000 chunk 350 optimal weight: 40.0000 chunk 173 optimal weight: 0.9990 chunk 314 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN ** B 544 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 762 GLN B 804 GLN B 913 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 81 ASN ** C 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN I 92 ASN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 30619 Z= 0.284 Angle : 0.640 10.856 41620 Z= 0.323 Chirality : 0.047 0.352 4853 Planarity : 0.005 0.057 5289 Dihedral : 5.801 52.110 5494 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.37 % Favored : 94.44 % Rotamer: Outliers : 2.52 % Allowed : 8.60 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.13), residues: 3634 helix: 0.71 (0.20), residues: 660 sheet: -0.41 (0.16), residues: 962 loop : -1.24 (0.13), residues: 2012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 53 HIS 0.004 0.001 HIS B1058 PHE 0.022 0.002 PHE B 86 TYR 0.022 0.001 TYR C 904 ARG 0.006 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 153 time to evaluate : 3.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7321 (m-80) cc_final: 0.7059 (m-80) REVERT: A 377 PHE cc_start: 0.3917 (OUTLIER) cc_final: 0.3621 (m-80) REVERT: E 105 ASP cc_start: -0.0590 (OUTLIER) cc_final: -0.1024 (m-30) REVERT: K 105 ASP cc_start: -0.4178 (OUTLIER) cc_final: -0.4758 (t0) REVERT: L 98 THR cc_start: 0.6335 (t) cc_final: 0.6086 (p) outliers start: 81 outliers final: 53 residues processed: 226 average time/residue: 0.4026 time to fit residues: 153.0283 Evaluate side-chains 192 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 136 time to evaluate : 3.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 195 LYS Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 407 VAL Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 105 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 292 optimal weight: 0.0370 chunk 199 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 144 optimal weight: 4.9990 chunk 299 optimal weight: 50.0000 chunk 242 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 179 optimal weight: 2.9990 chunk 314 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN A 762 GLN B 544 ASN B 762 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 762 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 30619 Z= 0.195 Angle : 0.584 9.501 41620 Z= 0.292 Chirality : 0.045 0.333 4853 Planarity : 0.004 0.046 5289 Dihedral : 5.429 52.522 5493 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 5.26 % Favored : 94.55 % Rotamer: Outliers : 2.31 % Allowed : 9.10 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.75 (0.14), residues: 3634 helix: 1.00 (0.20), residues: 666 sheet: -0.33 (0.16), residues: 969 loop : -1.10 (0.13), residues: 1999 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 53 HIS 0.004 0.001 HIS B 207 PHE 0.019 0.001 PHE B 86 TYR 0.019 0.001 TYR A1067 ARG 0.005 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 146 time to evaluate : 3.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 PHE cc_start: 0.7214 (m-80) cc_final: 0.6944 (m-80) REVERT: A 377 PHE cc_start: 0.4231 (OUTLIER) cc_final: 0.4004 (m-80) REVERT: B 332 ILE cc_start: 0.4068 (OUTLIER) cc_final: 0.3551 (mt) REVERT: E 83 MET cc_start: -0.0214 (mmt) cc_final: -0.0414 (mmt) REVERT: E 105 ASP cc_start: -0.0651 (OUTLIER) cc_final: -0.1039 (m-30) REVERT: L 4 MET cc_start: -0.0299 (ttm) cc_final: -0.1318 (mtp) outliers start: 74 outliers final: 48 residues processed: 211 average time/residue: 0.3779 time to fit residues: 136.5069 Evaluate side-chains 185 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 134 time to evaluate : 3.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 534 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 938 LEU Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain E residue 105 ASP Chi-restraints excluded: chain K residue 48 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 118 optimal weight: 3.9990 chunk 315 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 206 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 351 optimal weight: 9.9990 chunk 291 optimal weight: 0.4980 chunk 162 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 116 optimal weight: 0.0770 chunk 184 optimal weight: 5.9990 overall best weight: 1.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 755 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 121 ASN C 762 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30619 Z= 0.237 Angle : 0.594 10.448 41620 Z= 0.298 Chirality : 0.045 0.322 4853 Planarity : 0.004 0.052 5289 Dihedral : 5.376 54.014 5493 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.56 % Favored : 94.28 % Rotamer: Outliers : 2.62 % Allowed : 9.16 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: -0.69 (0.14), residues: 3634 helix: 1.13 (0.21), residues: 663 sheet: -0.29 (0.16), residues: 967 loop : -1.09 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 53 HIS 0.004 0.001 HIS B1058 PHE 0.022 0.002 PHE B 86 TYR 0.020 0.001 TYR A1067 ARG 0.009 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 147 time to evaluate : 3.544 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 377 PHE cc_start: 0.4160 (OUTLIER) cc_final: 0.3882 (m-80) REVERT: B 332 ILE cc_start: 0.4059 (OUTLIER) cc_final: 0.3412 (mt) REVERT: H 34 MET cc_start: 0.4749 (mmm) cc_final: 0.4456 (mmp) REVERT: K 105 ASP cc_start: -0.4146 (OUTLIER) cc_final: -0.4632 (t0) outliers start: 84 outliers final: 64 residues processed: 219 average time/residue: 0.4001 time to fit residues: 150.7525 Evaluate side-chains 201 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 134 time to evaluate : 3.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 578 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 735 SER Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 105 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 338 optimal weight: 40.0000 chunk 39 optimal weight: 7.9990 chunk 200 optimal weight: 6.9990 chunk 256 optimal weight: 6.9990 chunk 198 optimal weight: 10.0000 chunk 295 optimal weight: 0.7980 chunk 196 optimal weight: 4.9990 chunk 349 optimal weight: 7.9990 chunk 218 optimal weight: 0.9990 chunk 213 optimal weight: 0.0980 chunk 161 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 675 GLN ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN C1010 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.5547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 30619 Z= 0.204 Angle : 0.574 10.927 41620 Z= 0.287 Chirality : 0.045 0.316 4853 Planarity : 0.004 0.057 5289 Dihedral : 5.308 55.312 5493 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.28 % Favored : 94.61 % Rotamer: Outliers : 2.28 % Allowed : 9.98 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: -0.56 (0.14), residues: 3634 helix: 1.29 (0.21), residues: 667 sheet: -0.21 (0.16), residues: 959 loop : -1.03 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 53 HIS 0.003 0.001 HIS A1088 PHE 0.025 0.001 PHE B 429 TYR 0.019 0.001 TYR A1067 ARG 0.006 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 150 time to evaluate : 3.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 PHE cc_start: 0.4522 (OUTLIER) cc_final: 0.4211 (m-80) REVERT: A 902 MET cc_start: 0.7311 (tpt) cc_final: 0.7078 (tpt) REVERT: B 661 GLU cc_start: 0.6199 (OUTLIER) cc_final: 0.5673 (mm-30) REVERT: F 4 MET cc_start: 0.2290 (tpp) cc_final: 0.1901 (tpt) REVERT: K 105 ASP cc_start: -0.4140 (OUTLIER) cc_final: -0.4619 (t0) outliers start: 73 outliers final: 60 residues processed: 214 average time/residue: 0.3730 time to fit residues: 136.0706 Evaluate side-chains 203 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 140 time to evaluate : 3.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 368 LEU Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 661 GLU Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 105 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 216 optimal weight: 6.9990 chunk 139 optimal weight: 40.0000 chunk 208 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 222 optimal weight: 8.9990 chunk 238 optimal weight: 40.0000 chunk 172 optimal weight: 3.9990 chunk 32 optimal weight: 20.0000 chunk 275 optimal weight: 0.1980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 954 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 GLN C 762 GLN C1010 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 30619 Z= 0.229 Angle : 0.583 9.818 41620 Z= 0.292 Chirality : 0.045 0.311 4853 Planarity : 0.004 0.062 5289 Dihedral : 5.254 56.594 5492 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.50 % Favored : 94.36 % Rotamer: Outliers : 2.37 % Allowed : 10.29 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % 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: -0.56 (0.14), residues: 3634 helix: 1.30 (0.21), residues: 664 sheet: -0.19 (0.16), residues: 951 loop : -1.03 (0.14), residues: 2019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 53 HIS 0.003 0.001 HIS A 954 PHE 0.021 0.001 PHE A 86 TYR 0.023 0.001 TYR B 674 ARG 0.009 0.000 ARG B 983 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 139 time to evaluate : 3.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 377 PHE cc_start: 0.4306 (OUTLIER) cc_final: 0.4089 (m-80) REVERT: A 902 MET cc_start: 0.7380 (tpt) cc_final: 0.7127 (tpt) REVERT: A 1029 MET cc_start: 0.8295 (tpp) cc_final: 0.7977 (tpp) REVERT: B 52 GLN cc_start: 0.7138 (tm-30) cc_final: 0.6931 (tt0) REVERT: B 661 GLU cc_start: 0.6453 (tm-30) cc_final: 0.5936 (mm-30) REVERT: H 34 MET cc_start: 0.4644 (mmm) cc_final: 0.4212 (mmp) REVERT: K 105 ASP cc_start: -0.4085 (OUTLIER) cc_final: -0.4498 (t0) REVERT: L 98 THR cc_start: 0.6491 (t) cc_final: 0.6277 (p) outliers start: 76 outliers final: 61 residues processed: 206 average time/residue: 0.3761 time to fit residues: 133.5691 Evaluate side-chains 200 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 137 time to evaluate : 3.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 159 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 775 ASP Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 875 SER Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 105 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 318 optimal weight: 30.0000 chunk 335 optimal weight: 10.0000 chunk 305 optimal weight: 40.0000 chunk 326 optimal weight: 30.0000 chunk 196 optimal weight: 0.9990 chunk 142 optimal weight: 4.9990 chunk 256 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 308 optimal weight: 9.9990 chunk 324 optimal weight: 20.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1088 HIS ** B 125 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 354 ASN B 675 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 955 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 762 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.6094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.110 30619 Z= 0.464 Angle : 0.710 14.967 41620 Z= 0.358 Chirality : 0.049 0.312 4853 Planarity : 0.005 0.070 5289 Dihedral : 5.922 59.760 5492 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.15 % Favored : 92.71 % Rotamer: Outliers : 2.49 % Allowed : 10.50 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.14), residues: 3634 helix: 0.89 (0.20), residues: 657 sheet: -0.47 (0.16), residues: 964 loop : -1.20 (0.14), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 64 HIS 0.008 0.001 HIS A1048 PHE 0.029 0.002 PHE C 86 TYR 0.037 0.002 TYR C 904 ARG 0.007 0.001 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 135 time to evaluate : 4.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 TRP cc_start: 0.6452 (m-90) cc_final: 0.5565 (m-90) REVERT: A 377 PHE cc_start: 0.4243 (OUTLIER) cc_final: 0.3952 (m-80) REVERT: A 1029 MET cc_start: 0.8272 (tpp) cc_final: 0.8001 (tpp) REVERT: B 389 ASP cc_start: 0.6636 (OUTLIER) cc_final: 0.4896 (t70) REVERT: C 368 LEU cc_start: 0.4922 (OUTLIER) cc_final: 0.4280 (tp) REVERT: F 4 MET cc_start: 0.2606 (tpp) cc_final: 0.2138 (tpt) REVERT: H 34 MET cc_start: 0.4893 (mmm) cc_final: 0.4514 (mmp) REVERT: K 105 ASP cc_start: -0.4073 (OUTLIER) cc_final: -0.4540 (t0) outliers start: 80 outliers final: 64 residues processed: 205 average time/residue: 0.3711 time to fit residues: 131.0619 Evaluate side-chains 193 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 125 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 377 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 544 ASN Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 731 MET Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 794 ILE Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 960 ASN Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain B residue 1114 ILE Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain E residue 99 VAL Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 105 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 214 optimal weight: 3.9990 chunk 344 optimal weight: 8.9990 chunk 210 optimal weight: 4.9990 chunk 163 optimal weight: 0.9980 chunk 239 optimal weight: 50.0000 chunk 361 optimal weight: 30.0000 chunk 332 optimal weight: 5.9990 chunk 287 optimal weight: 0.7980 chunk 29 optimal weight: 10.0000 chunk 222 optimal weight: 4.9990 chunk 176 optimal weight: 0.9980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 762 GLN A 954 HIS ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 955 ASN C 690 GLN C 762 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.6220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 30619 Z= 0.278 Angle : 0.615 13.723 41620 Z= 0.308 Chirality : 0.046 0.310 4853 Planarity : 0.005 0.070 5289 Dihedral : 5.695 59.743 5492 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.42 % Favored : 94.44 % Rotamer: Outliers : 2.06 % Allowed : 11.16 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.76 (0.14), residues: 3634 helix: 1.10 (0.21), residues: 662 sheet: -0.35 (0.16), residues: 975 loop : -1.14 (0.14), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 53 HIS 0.005 0.001 HIS A 954 PHE 0.021 0.002 PHE B 86 TYR 0.029 0.001 TYR C 904 ARG 0.004 0.000 ARG A 905 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7268 Ramachandran restraints generated. 3634 Oldfield, 0 Emsley, 3634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 134 time to evaluate : 3.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1029 MET cc_start: 0.8261 (tpp) cc_final: 0.8008 (tpp) REVERT: B 200 TYR cc_start: 0.5622 (OUTLIER) cc_final: 0.4832 (m-80) REVERT: B 389 ASP cc_start: 0.6590 (OUTLIER) cc_final: 0.4781 (t70) REVERT: C 158 ARG cc_start: 0.6314 (OUTLIER) cc_final: 0.5230 (ptt90) REVERT: C 368 LEU cc_start: 0.4859 (OUTLIER) cc_final: 0.4215 (tp) REVERT: E 83 MET cc_start: -0.0227 (mmt) cc_final: -0.0499 (mmt) REVERT: F 4 MET cc_start: 0.2634 (tpp) cc_final: 0.2175 (tpt) REVERT: H 34 MET cc_start: 0.4652 (mmm) cc_final: 0.4357 (mmp) REVERT: K 105 ASP cc_start: -0.3949 (OUTLIER) cc_final: -0.4400 (t0) outliers start: 66 outliers final: 58 residues processed: 194 average time/residue: 0.3698 time to fit residues: 123.0743 Evaluate side-chains 191 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 128 time to evaluate : 3.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 122 ASN Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 294 ASP Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 558 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 610 VAL Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 773 GLU Chi-restraints excluded: chain A residue 855 PHE Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1027 THR Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 331 ASN Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 389 ASP Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 552 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 611 LEU Chi-restraints excluded: chain B residue 642 VAL Chi-restraints excluded: chain B residue 705 VAL Chi-restraints excluded: chain B residue 749 CYS Chi-restraints excluded: chain B residue 751 ASN Chi-restraints excluded: chain B residue 780 GLU Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 1006 THR Chi-restraints excluded: chain C residue 125 ASN Chi-restraints excluded: chain C residue 158 ARG Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 368 LEU Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 586 ASP Chi-restraints excluded: chain C residue 617 CYS Chi-restraints excluded: chain C residue 620 VAL Chi-restraints excluded: chain C residue 649 CYS Chi-restraints excluded: chain C residue 734 THR Chi-restraints excluded: chain C residue 875 SER Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 968 SER Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1100 THR Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1130 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 105 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 363 random chunks: chunk 228 optimal weight: 30.0000 chunk 306 optimal weight: 40.0000 chunk 88 optimal weight: 0.8980 chunk 265 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 288 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 chunk 36 optimal weight: 30.0000 chunk 53 optimal weight: 9.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 564 GLN ** B 804 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 690 GLN C 762 GLN ** F 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.195481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.124038 restraints weight = 53241.241| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 4.68 r_work: 0.3370 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.6319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 30619 Z= 0.220 Angle : 0.589 11.624 41620 Z= 0.294 Chirality : 0.045 0.306 4853 Planarity : 0.005 0.070 5289 Dihedral : 5.504 59.951 5492 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.61 % Favored : 94.25 % Rotamer: Outliers : 2.09 % Allowed : 11.19 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.14), residues: 3634 helix: 1.38 (0.21), residues: 654 sheet: -0.20 (0.16), residues: 967 loop : -1.09 (0.14), residues: 2013 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 53 HIS 0.006 0.001 HIS A 954 PHE 0.025 0.001 PHE A 168 TYR 0.024 0.001 TYR C 904 ARG 0.009 0.000 ARG B 983 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6084.62 seconds wall clock time: 111 minutes 56.86 seconds (6716.86 seconds total)