Starting phenix.real_space_refine on Sat Feb 17 21:14:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vo1_21257/02_2024/6vo1_21257.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vo1_21257/02_2024/6vo1_21257.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vo1_21257/02_2024/6vo1_21257.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vo1_21257/02_2024/6vo1_21257.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vo1_21257/02_2024/6vo1_21257.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vo1_21257/02_2024/6vo1_21257.pdb" } resolution = 3.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.073 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 123 5.16 5 C 12396 2.51 5 N 3300 2.21 5 O 3987 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L GLU 55": "OE1" <-> "OE2" Residue "J GLU 55": "OE1" <-> "OE2" Residue "K GLU 55": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 19806 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3470 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "B" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1033 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Chain: "H" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 896 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "C" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3470 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "E" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1033 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Chain: "G" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 896 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "J" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 3470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3470 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 22, 'TRANS': 417} Chain breaks: 3 Chain: "F" Number of atoms: 1033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1033 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 2, 'TRANS': 126} Chain breaks: 1 Chain: "I" Number of atoms: 896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 896 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "K" Number of atoms: 812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 812 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 99} 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "a" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "g" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "h" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "i" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "j" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "k" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "l" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "m" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "D" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 9.70, per 1000 atoms: 0.49 Number of scatterers: 19806 At special positions: 0 Unit cell: (170.2, 166.75, 119.6, 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 123 16.00 O 3987 8.00 N 3300 7.00 C 12396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 73 " distance=2.15 Simple disulfide: pdb=" SG CYS A 74 " - pdb=" SG CYS B 561 " distance=2.03 Simple disulfide: pdb=" SG CYS A 119 " - pdb=" SG CYS A 205 " distance=2.04 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 157 " distance=2.02 Simple disulfide: pdb=" SG CYS A 218 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 239 " distance=2.04 Simple disulfide: pdb=" SG CYS A 296 " - pdb=" SG CYS A 331 " distance=2.03 Simple disulfide: pdb=" SG CYS A 378 " - pdb=" SG CYS A 445 " distance=2.02 Simple disulfide: pdb=" SG CYS A 385 " - pdb=" SG CYS A 418 " distance=2.03 Simple disulfide: pdb=" SG CYS A 501 " - pdb=" SG CYS B 605 " distance=2.03 Simple disulfide: pdb=" SG CYS B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 73 " distance=2.15 Simple disulfide: pdb=" SG CYS C 74 " - pdb=" SG CYS E 561 " distance=2.03 Simple disulfide: pdb=" SG CYS C 119 " - pdb=" SG CYS C 205 " distance=2.04 Simple disulfide: pdb=" SG CYS C 126 " - pdb=" SG CYS C 196 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 157 " distance=2.02 Simple disulfide: pdb=" SG CYS C 218 " - pdb=" SG CYS C 247 " distance=2.03 Simple disulfide: pdb=" SG CYS C 228 " - pdb=" SG CYS C 239 " distance=2.04 Simple disulfide: pdb=" SG CYS C 296 " - pdb=" SG CYS C 331 " distance=2.03 Simple disulfide: pdb=" SG CYS C 378 " - pdb=" SG CYS C 445 " distance=2.02 Simple disulfide: pdb=" SG CYS C 385 " - pdb=" SG CYS C 418 " distance=2.03 Simple disulfide: pdb=" SG CYS C 501 " - pdb=" SG CYS E 605 " distance=2.03 Simple disulfide: pdb=" SG CYS E 598 " - pdb=" SG CYS E 604 " distance=2.02 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 73 " distance=2.15 Simple disulfide: pdb=" SG CYS D 74 " - pdb=" SG CYS F 561 " distance=2.03 Simple disulfide: pdb=" SG CYS D 119 " - pdb=" SG CYS D 205 " distance=2.04 Simple disulfide: pdb=" SG CYS D 126 " - pdb=" SG CYS D 196 " distance=2.03 Simple disulfide: pdb=" SG CYS D 131 " - pdb=" SG CYS D 157 " distance=2.02 Simple disulfide: pdb=" SG CYS D 218 " - pdb=" SG CYS D 247 " distance=2.03 Simple disulfide: pdb=" SG CYS D 228 " - pdb=" SG CYS D 239 " distance=2.04 Simple disulfide: pdb=" SG CYS D 296 " - pdb=" SG CYS D 331 " distance=2.03 Simple disulfide: pdb=" SG CYS D 378 " - pdb=" SG CYS D 445 " distance=2.02 Simple disulfide: pdb=" SG CYS D 385 " - pdb=" SG CYS D 418 " distance=2.03 Simple disulfide: pdb=" SG CYS D 501 " - pdb=" SG CYS F 605 " distance=2.03 Simple disulfide: pdb=" SG CYS F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 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 ALPHA1-2 " MAN Q 4 " - " MAN Q 5 " " MAN Z 4 " - " MAN Z 5 " " MAN i 4 " - " MAN i 5 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA Z 3 " - " MAN Z 4 " " BMA i 3 " - " MAN i 4 " ALPHA1-6 " BMA Q 3 " - " MAN Q 6 " " BMA Z 3 " - " MAN Z 6 " " BMA i 3 " - " MAN i 6 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG V 1 " - " NAG V 2 " " NAG W 1 " - " NAG W 2 " " NAG W 2 " - " BMA W 3 " " NAG X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Z 1 " - " NAG Z 2 " " NAG Z 2 " - " BMA Z 3 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG f 2 " - " BMA f 3 " " NAG g 1 " - " NAG g 2 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG i 2 " - " BMA i 3 " " NAG j 1 " - " NAG j 2 " " NAG k 1 " - " NAG k 2 " " NAG l 1 " - " NAG l 2 " " NAG m 1 " - " NAG m 2 " NAG-ASN " NAG A 618 " - " ASN A 295 " " NAG A 621 " - " ASN A 386 " " NAG A 626 " - " ASN A 355 " " NAG A 627 " - " ASN A 339 " " NAG A 628 " - " ASN A 133 " " NAG A 629 " - " ASN A 197 " " NAG C 618 " - " ASN C 295 " " NAG C 621 " - " ASN C 386 " " NAG C 626 " - " ASN C 355 " " NAG C 627 " - " ASN C 339 " " NAG C 628 " - " ASN C 133 " " NAG C 629 " - " ASN C 197 " " NAG D 618 " - " ASN D 295 " " NAG D 621 " - " ASN D 386 " " NAG D 626 " - " ASN D 355 " " NAG D 627 " - " ASN D 339 " " NAG D 628 " - " ASN D 133 " " NAG D 629 " - " ASN D 197 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 156 " " NAG O 1 " - " ASN A 160 " " NAG P 1 " - " ASN A 234 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 276 " " NAG S 1 " - " ASN A 332 " " NAG T 1 " - " ASN A 392 " " NAG U 1 " - " ASN A 448 " " NAG V 1 " - " ASN C 88 " " NAG W 1 " - " ASN C 156 " " NAG X 1 " - " ASN C 160 " " NAG Y 1 " - " ASN C 234 " " NAG Z 1 " - " ASN C 262 " " NAG a 1 " - " ASN C 276 " " NAG b 1 " - " ASN C 332 " " NAG c 1 " - " ASN C 392 " " NAG d 1 " - " ASN C 448 " " NAG e 1 " - " ASN D 88 " " NAG f 1 " - " ASN D 156 " " NAG g 1 " - " ASN D 160 " " NAG h 1 " - " ASN D 234 " " NAG i 1 " - " ASN D 262 " " NAG j 1 " - " ASN D 276 " " NAG k 1 " - " ASN D 332 " " NAG l 1 " - " ASN D 392 " " NAG m 1 " - " ASN D 448 " Time building additional restraints: 8.20 Conformation dependent library (CDL) restraints added in 3.4 seconds 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4428 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 45 sheets defined 22.7% alpha, 35.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.49 Creating SS restraints... Processing helix chain 'A' and resid 67 through 73 Processing helix chain 'A' and resid 98 through 117 removed outlier: 3.582A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 Processing helix chain 'A' and resid 139 through 151 Processing helix chain 'A' and resid 195 through 198 Processing helix chain 'A' and resid 335 through 350 Processing helix chain 'A' and resid 351 through 353 No H-bonds generated for 'chain 'A' and resid 351 through 353' Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 390 Processing helix chain 'A' and resid 474 through 478 Processing helix chain 'A' and resid 479 through 484 Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 560 through 565 Processing helix chain 'B' and resid 569 through 596 Processing helix chain 'B' and resid 618 through 623 Processing helix chain 'B' and resid 627 through 635 Processing helix chain 'B' and resid 638 through 661 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'C' and resid 67 through 73 Processing helix chain 'C' and resid 98 through 117 removed outlier: 3.582A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 126 Processing helix chain 'C' and resid 139 through 151 Processing helix chain 'C' and resid 195 through 198 Processing helix chain 'C' and resid 335 through 350 Processing helix chain 'C' and resid 351 through 353 No H-bonds generated for 'chain 'C' and resid 351 through 353' Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 390 Processing helix chain 'C' and resid 474 through 478 Processing helix chain 'C' and resid 479 through 484 Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 536 through 542 Processing helix chain 'E' and resid 560 through 565 Processing helix chain 'E' and resid 569 through 596 Processing helix chain 'E' and resid 618 through 623 Processing helix chain 'E' and resid 627 through 635 Processing helix chain 'E' and resid 638 through 661 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'D' and resid 67 through 73 Processing helix chain 'D' and resid 98 through 117 removed outlier: 3.581A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 126 Processing helix chain 'D' and resid 139 through 151 Processing helix chain 'D' and resid 195 through 198 Processing helix chain 'D' and resid 335 through 350 Processing helix chain 'D' and resid 351 through 353 No H-bonds generated for 'chain 'D' and resid 351 through 353' Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 390 Processing helix chain 'D' and resid 474 through 478 Processing helix chain 'D' and resid 479 through 484 Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 560 through 565 Processing helix chain 'F' and resid 569 through 596 Processing helix chain 'F' and resid 618 through 623 Processing helix chain 'F' and resid 627 through 635 Processing helix chain 'F' and resid 638 through 661 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'K' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 499 removed outlier: 4.850A pdb=" N VAL B 608 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N VAL A 38 " --> pdb=" O THR B 606 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR B 606 " --> pdb=" O VAL A 38 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR A 40 " --> pdb=" O CYS B 604 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N CYS B 604 " --> pdb=" O TYR A 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 4.610A pdb=" N VAL A 242 " --> pdb=" O LEU A 86 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA4, first strand: chain 'A' and resid 130 through 133 Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 183 Processing sheet with id=AA6, first strand: chain 'A' and resid 259 through 261 removed outlier: 6.611A pdb=" N LEU A 260 " --> pdb=" O THR A 450 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 10.242A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN A 293 " --> pdb=" O SER A 334 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 329 " --> pdb=" O CYS A 418 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.958A pdb=" N THR A 450 " --> pdb=" O PHE A 288 " (cutoff:3.500A) removed outlier: 9.796A pdb=" N THR A 290 " --> pdb=" O ASN A 448 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN A 448 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 10.242A pdb=" N VAL A 292 " --> pdb=" O VAL A 446 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N VAL A 446 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE A 294 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N ARG A 444 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N CYS A 296 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL A 442 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 307 through 312 removed outlier: 6.518A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 361 Processing sheet with id=AB1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.095A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE H 48 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR H 59 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN H 50 " --> pdb=" O THR H 57 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR H 57 " --> pdb=" O ASN H 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 11 through 12 removed outlier: 7.074A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.232A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.232A pdb=" N LEU L 11 " --> pdb=" O ASP L 105 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 494 through 499 removed outlier: 4.850A pdb=" N VAL E 608 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N VAL C 38 " --> pdb=" O THR E 606 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR E 606 " --> pdb=" O VAL C 38 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR C 40 " --> pdb=" O CYS E 604 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N CYS E 604 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 45 through 47 removed outlier: 4.610A pdb=" N VAL C 242 " --> pdb=" O LEU C 86 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC1, first strand: chain 'C' and resid 130 through 133 Processing sheet with id=AC2, first strand: chain 'C' and resid 181 through 183 Processing sheet with id=AC3, first strand: chain 'C' and resid 259 through 261 removed outlier: 6.611A pdb=" N LEU C 260 " --> pdb=" O THR C 450 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN C 293 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 329 " --> pdb=" O CYS C 418 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.957A pdb=" N THR C 450 " --> pdb=" O PHE C 288 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N THR C 290 " --> pdb=" O ASN C 448 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN C 448 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N VAL C 292 " --> pdb=" O VAL C 446 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N VAL C 446 " --> pdb=" O VAL C 292 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE C 294 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N ARG C 444 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N CYS C 296 " --> pdb=" O VAL C 442 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N VAL C 442 " --> pdb=" O CYS C 296 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 307 through 312 removed outlier: 6.518A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 360 through 361 Processing sheet with id=AC7, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AC8, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.096A pdb=" N ARG G 38 " --> pdb=" O TRP G 47 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N TRP G 47 " --> pdb=" O ARG G 38 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE G 48 " --> pdb=" O TYR G 59 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR G 59 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN G 50 " --> pdb=" O THR G 57 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR G 57 " --> pdb=" O ASN G 50 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 11 through 12 removed outlier: 7.073A pdb=" N CYS G 92 " --> pdb=" O TRP G 103 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TRP G 103 " --> pdb=" O CYS G 92 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG G 94 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.232A pdb=" N LEU J 11 " --> pdb=" O ASP J 105 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.232A pdb=" N LEU J 11 " --> pdb=" O ASP J 105 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 494 through 499 removed outlier: 4.850A pdb=" N VAL F 608 " --> pdb=" O VAL D 36 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N VAL D 38 " --> pdb=" O THR F 606 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N THR F 606 " --> pdb=" O VAL D 38 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N TYR D 40 " --> pdb=" O CYS F 604 " (cutoff:3.500A) removed outlier: 8.503A pdb=" N CYS F 604 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 45 through 47 removed outlier: 4.610A pdb=" N VAL D 242 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AD7, first strand: chain 'D' and resid 130 through 133 Processing sheet with id=AD8, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AD9, first strand: chain 'D' and resid 259 through 261 removed outlier: 6.611A pdb=" N LEU D 260 " --> pdb=" O THR D 450 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N GLN D 293 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA D 329 " --> pdb=" O CYS D 418 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 271 through 274 removed outlier: 6.958A pdb=" N THR D 450 " --> pdb=" O PHE D 288 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N THR D 290 " --> pdb=" O ASN D 448 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ASN D 448 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N VAL D 292 " --> pdb=" O VAL D 446 " (cutoff:3.500A) removed outlier: 9.436A pdb=" N VAL D 446 " --> pdb=" O VAL D 292 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ILE D 294 " --> pdb=" O ARG D 444 " (cutoff:3.500A) removed outlier: 9.968A pdb=" N ARG D 444 " --> pdb=" O ILE D 294 " (cutoff:3.500A) removed outlier: 11.205A pdb=" N CYS D 296 " --> pdb=" O VAL D 442 " (cutoff:3.500A) removed outlier: 10.380A pdb=" N VAL D 442 " --> pdb=" O CYS D 296 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 307 through 312 removed outlier: 6.518A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 360 through 361 Processing sheet with id=AE4, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.096A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE I 48 " --> pdb=" O TYR I 59 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR I 59 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ASN I 50 " --> pdb=" O THR I 57 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N THR I 57 " --> pdb=" O ASN I 50 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'I' and resid 11 through 12 removed outlier: 7.074A pdb=" N CYS I 92 " --> pdb=" O TRP I 103 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N TRP I 103 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARG I 94 " --> pdb=" O ASP I 101 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 4 through 7 Processing sheet with id=AE8, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.232A pdb=" N LEU K 11 " --> pdb=" O ASP K 105 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N TRP K 35 " --> pdb=" O LEU K 47 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'K' and resid 10 through 13 removed outlier: 6.232A pdb=" N LEU K 11 " --> pdb=" O ASP K 105 " (cutoff:3.500A) 786 hydrogen bonds defined for protein. 1953 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: 6.80 Time building geometry restraints manager: 8.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4204 1.32 - 1.45: 6292 1.45 - 1.58: 9547 1.58 - 1.72: 6 1.72 - 1.85: 156 Bond restraints: 20205 Sorted by residual: bond pdb=" CB TYR J 50 " pdb=" CG TYR J 50 " ideal model delta sigma weight residual 1.512 1.399 0.113 2.20e-02 2.07e+03 2.66e+01 bond pdb=" CB TYR L 50 " pdb=" CG TYR L 50 " ideal model delta sigma weight residual 1.512 1.399 0.113 2.20e-02 2.07e+03 2.66e+01 bond pdb=" CB TYR K 50 " pdb=" CG TYR K 50 " ideal model delta sigma weight residual 1.512 1.399 0.113 2.20e-02 2.07e+03 2.64e+01 bond pdb=" CB TYR K 36 " pdb=" CG TYR K 36 " ideal model delta sigma weight residual 1.512 1.400 0.112 2.20e-02 2.07e+03 2.60e+01 bond pdb=" CB TYR J 36 " pdb=" CG TYR J 36 " ideal model delta sigma weight residual 1.512 1.400 0.112 2.20e-02 2.07e+03 2.59e+01 ... (remaining 20200 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.78: 1029 106.78 - 113.59: 10977 113.59 - 120.39: 8031 120.39 - 127.20: 7139 127.20 - 134.00: 277 Bond angle restraints: 27453 Sorted by residual: angle pdb=" N SER F 613 " pdb=" CA SER F 613 " pdb=" C SER F 613 " ideal model delta sigma weight residual 114.62 101.95 12.67 1.14e+00 7.69e-01 1.24e+02 angle pdb=" N SER E 613 " pdb=" CA SER E 613 " pdb=" C SER E 613 " ideal model delta sigma weight residual 114.62 101.95 12.67 1.14e+00 7.69e-01 1.24e+02 angle pdb=" N SER B 613 " pdb=" CA SER B 613 " pdb=" C SER B 613 " ideal model delta sigma weight residual 114.62 101.97 12.65 1.14e+00 7.69e-01 1.23e+02 angle pdb=" N PHE D 53 " pdb=" CA PHE D 53 " pdb=" C PHE D 53 " ideal model delta sigma weight residual 111.36 122.40 -11.04 1.09e+00 8.42e-01 1.03e+02 angle pdb=" N PHE A 53 " pdb=" CA PHE A 53 " pdb=" C PHE A 53 " ideal model delta sigma weight residual 111.36 122.39 -11.03 1.09e+00 8.42e-01 1.02e+02 ... (remaining 27448 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.72: 12651 21.72 - 43.43: 375 43.43 - 65.15: 129 65.15 - 86.86: 51 86.86 - 108.58: 27 Dihedral angle restraints: 13233 sinusoidal: 6369 harmonic: 6864 Sorted by residual: dihedral pdb=" CB CYS D 126 " pdb=" SG CYS D 126 " pdb=" SG CYS D 196 " pdb=" CB CYS D 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.29 -57.29 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CB CYS A 126 " pdb=" SG CYS A 126 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.28 -57.28 1 1.00e+01 1.00e-02 4.41e+01 dihedral pdb=" CB CYS C 126 " pdb=" SG CYS C 126 " pdb=" SG CYS C 196 " pdb=" CB CYS C 196 " ideal model delta sinusoidal sigma weight residual 93.00 150.25 -57.25 1 1.00e+01 1.00e-02 4.41e+01 ... (remaining 13230 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 2574 0.113 - 0.226: 687 0.226 - 0.338: 87 0.338 - 0.451: 0 0.451 - 0.564: 6 Chirality restraints: 3354 Sorted by residual: chirality pdb=" C1 BMA f 3 " pdb=" O4 NAG f 2 " pdb=" C2 BMA f 3 " pdb=" O5 BMA f 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.33e+01 chirality pdb=" C1 BMA Z 3 " pdb=" O4 NAG Z 2 " pdb=" C2 BMA Z 3 " pdb=" O5 BMA Z 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.32e+01 chirality pdb=" C1 BMA i 3 " pdb=" O4 NAG i 2 " pdb=" C2 BMA i 3 " pdb=" O5 BMA i 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.56 0.16 2.00e-02 2.50e+03 6.32e+01 ... (remaining 3351 not shown) Planarity restraints: 3411 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 392 " -0.057 2.00e-02 2.50e+03 5.89e-02 4.34e+01 pdb=" CG ASN D 392 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN D 392 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN D 392 " 0.092 2.00e-02 2.50e+03 pdb=" C1 NAG l 1 " -0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN C 392 " 0.056 2.00e-02 2.50e+03 5.87e-02 4.31e+01 pdb=" CG ASN C 392 " -0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN C 392 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN C 392 " -0.091 2.00e-02 2.50e+03 pdb=" C1 NAG c 1 " 0.070 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 392 " -0.056 2.00e-02 2.50e+03 5.87e-02 4.30e+01 pdb=" CG ASN A 392 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASN A 392 " 0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 392 " 0.091 2.00e-02 2.50e+03 pdb=" C1 NAG T 1 " -0.070 2.00e-02 2.50e+03 ... (remaining 3408 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 335 2.61 - 3.18: 17911 3.18 - 3.75: 31236 3.75 - 4.33: 45173 4.33 - 4.90: 70376 Nonbonded interactions: 165031 Sorted by model distance: nonbonded pdb=" CZ PHE A 288 " pdb=" CD1 LEU A 452 " model vdw 2.033 3.760 nonbonded pdb=" CZ PHE C 288 " pdb=" CD1 LEU C 452 " model vdw 2.034 3.760 nonbonded pdb=" CZ PHE D 288 " pdb=" CD1 LEU D 452 " model vdw 2.035 3.760 nonbonded pdb=" OG1 THR A 357 " pdb=" OG1 THR A 465 " model vdw 2.314 2.440 nonbonded pdb=" OG1 THR C 357 " pdb=" OG1 THR C 465 " model vdw 2.314 2.440 ... (remaining 165026 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'X' selection = chain 'Y' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'g' selection = chain 'h' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' } ncs_group { reference = chain 'N' selection = chain 'W' selection = chain 'f' } ncs_group { reference = chain 'Q' selection = chain 'Z' selection = chain 'i' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.040 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: 0.010 Extract box with map and model: 6.160 Check model and map are aligned: 0.260 Set scattering table: 0.150 Process input model: 50.900 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 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 : 0.020 0.123 20205 Z= 1.323 Angle : 1.809 12.674 27453 Z= 1.162 Chirality : 0.101 0.564 3354 Planarity : 0.009 0.049 3366 Dihedral : 13.289 108.579 8679 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 1.29 % Allowed : 4.50 % Favored : 94.22 % Rotamer: Outliers : 0.72 % Allowed : 0.57 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.17), residues: 2334 helix: -0.19 (0.23), residues: 453 sheet: 0.58 (0.19), residues: 681 loop : -0.10 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.010 TRP J 35 HIS 0.017 0.003 HIS C 374 PHE 0.032 0.006 PHE I 78 TYR 0.045 0.010 TYR J 36 ARG 0.006 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 418 time to evaluate : 2.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8941 (mt) cc_final: 0.8490 (mt) REVERT: A 150 MET cc_start: 0.8770 (mmm) cc_final: 0.8450 (mmt) REVERT: B 539 VAL cc_start: 0.9160 (t) cc_final: 0.8612 (t) REVERT: B 588 ARG cc_start: 0.8549 (mtt180) cc_final: 0.8214 (mtt180) REVERT: L 93 ASN cc_start: 0.9074 (t0) cc_final: 0.8804 (m110) REVERT: C 52 LEU cc_start: 0.8937 (mt) cc_final: 0.8259 (mt) REVERT: E 539 VAL cc_start: 0.9198 (t) cc_final: 0.8769 (t) REVERT: E 586 TYR cc_start: 0.9305 (t80) cc_final: 0.9050 (t80) REVERT: E 588 ARG cc_start: 0.8409 (mtt180) cc_final: 0.8165 (mtt180) REVERT: D 52 LEU cc_start: 0.8939 (mt) cc_final: 0.8681 (mt) REVERT: D 112 TRP cc_start: 0.8410 (t-100) cc_final: 0.8030 (t-100) REVERT: D 150 MET cc_start: 0.8793 (mmm) cc_final: 0.8577 (mmp) REVERT: F 588 ARG cc_start: 0.8400 (mtt180) cc_final: 0.8108 (mtt180) REVERT: K 93 ASN cc_start: 0.9048 (t0) cc_final: 0.8830 (m-40) outliers start: 15 outliers final: 9 residues processed: 433 average time/residue: 0.3595 time to fit residues: 228.2614 Evaluate side-chains 199 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 190 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 339 ASN Chi-restraints excluded: chain C residue 412 ASP Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 412 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 181 optimal weight: 0.0980 chunk 70 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 209 optimal weight: 2.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 HIS ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN C 352 HIS C 377 ASN ** E 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 105 GLN J 92 ASN ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20205 Z= 0.248 Angle : 0.784 11.874 27453 Z= 0.401 Chirality : 0.047 0.227 3354 Planarity : 0.004 0.034 3366 Dihedral : 10.111 81.225 4344 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.78 % Favored : 93.57 % Rotamer: Outliers : 1.91 % Allowed : 7.84 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.20 (0.17), residues: 2334 helix: 0.25 (0.24), residues: 474 sheet: 0.53 (0.19), residues: 681 loop : -0.63 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP B 628 HIS 0.003 0.001 HIS I 53 PHE 0.016 0.002 PHE G 78 TYR 0.018 0.002 TYR J 50 ARG 0.008 0.001 ARG I 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 267 time to evaluate : 2.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TRP cc_start: 0.8148 (t-100) cc_final: 0.7856 (t-100) REVERT: A 150 MET cc_start: 0.8724 (mmm) cc_final: 0.8442 (mmt) REVERT: A 427 TRP cc_start: 0.8217 (m-90) cc_final: 0.7953 (m-90) REVERT: B 626 MET cc_start: 0.8049 (ttm) cc_final: 0.6186 (mtp) REVERT: L 70 ASP cc_start: 0.8531 (m-30) cc_final: 0.8084 (p0) REVERT: J 89 GLN cc_start: 0.8339 (pp30) cc_final: 0.8063 (pp30) REVERT: D 150 MET cc_start: 0.8820 (mmm) cc_final: 0.8458 (mmp) REVERT: D 161 MET cc_start: 0.8589 (tpt) cc_final: 0.8292 (tpt) REVERT: F 545 LEU cc_start: 0.8872 (mt) cc_final: 0.8581 (tp) REVERT: F 656 ASN cc_start: 0.9537 (m-40) cc_final: 0.9240 (m-40) REVERT: K 49 TYR cc_start: 0.8903 (p90) cc_final: 0.8552 (p90) REVERT: K 89 GLN cc_start: 0.8476 (pp30) cc_final: 0.7885 (pp30) outliers start: 40 outliers final: 19 residues processed: 298 average time/residue: 0.3390 time to fit residues: 151.4908 Evaluate side-chains 208 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 189 time to evaluate : 2.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 339 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 96 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain K residue 82 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 116 optimal weight: 0.2980 chunk 65 optimal weight: 10.0000 chunk 174 optimal weight: 3.9990 chunk 142 optimal weight: 9.9990 chunk 57 optimal weight: 7.9990 chunk 210 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 187 optimal weight: 0.7980 chunk 208 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 168 optimal weight: 8.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 105 GLN L 89 GLN L 92 ASN ** C 72 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN G 105 GLN D 352 HIS ** F 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 105 GLN K 92 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.3525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 20205 Z= 0.327 Angle : 0.750 12.444 27453 Z= 0.376 Chirality : 0.046 0.345 3354 Planarity : 0.004 0.058 3366 Dihedral : 8.096 67.732 4332 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.51 % Allowed : 6.08 % Favored : 93.40 % Rotamer: Outliers : 2.39 % Allowed : 9.33 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.17), residues: 2334 helix: 0.72 (0.25), residues: 456 sheet: 0.38 (0.19), residues: 681 loop : -0.77 (0.17), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP E 571 HIS 0.006 0.002 HIS L 91 PHE 0.017 0.002 PHE C 288 TYR 0.030 0.002 TYR J 50 ARG 0.006 0.001 ARG I 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 196 time to evaluate : 2.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TRP cc_start: 0.8383 (t-100) cc_final: 0.8065 (t-100) REVERT: A 150 MET cc_start: 0.8738 (mmm) cc_final: 0.8342 (mmt) REVERT: L 70 ASP cc_start: 0.8573 (m-30) cc_final: 0.8104 (p0) REVERT: D 150 MET cc_start: 0.8828 (mmm) cc_final: 0.8369 (mmt) REVERT: F 545 LEU cc_start: 0.9000 (mt) cc_final: 0.8794 (tp) REVERT: F 571 TRP cc_start: 0.8677 (m-90) cc_final: 0.8404 (m-90) REVERT: F 656 ASN cc_start: 0.9488 (m-40) cc_final: 0.9185 (m-40) REVERT: K 49 TYR cc_start: 0.9133 (p90) cc_final: 0.8818 (p90) REVERT: K 78 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9383 (mt) outliers start: 50 outliers final: 30 residues processed: 226 average time/residue: 0.3221 time to fit residues: 112.0586 Evaluate side-chains 195 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 164 time to evaluate : 2.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 125 LEU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 536 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 536 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 546 SER Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain K residue 78 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 207 optimal weight: 5.9990 chunk 158 optimal weight: 0.0770 chunk 109 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 141 optimal weight: 10.0000 chunk 210 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 110 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.0140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN L 91 HIS F 543 ASN K 91 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20205 Z= 0.178 Angle : 0.651 8.392 27453 Z= 0.324 Chirality : 0.045 0.357 3354 Planarity : 0.003 0.036 3366 Dihedral : 7.158 59.071 4332 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.47 % Allowed : 5.70 % Favored : 93.83 % Rotamer: Outliers : 1.96 % Allowed : 9.66 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.17), residues: 2334 helix: 0.83 (0.25), residues: 459 sheet: 0.49 (0.21), residues: 609 loop : -0.70 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP C 427 HIS 0.005 0.001 HIS C 105 PHE 0.013 0.001 PHE G 78 TYR 0.031 0.002 TYR K 50 ARG 0.008 0.000 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 199 time to evaluate : 2.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TRP cc_start: 0.8361 (t-100) cc_final: 0.8054 (t-100) REVERT: A 150 MET cc_start: 0.8718 (mmm) cc_final: 0.8370 (mmt) REVERT: A 161 MET cc_start: 0.8245 (tpt) cc_final: 0.8029 (tpt) REVERT: B 596 TRP cc_start: 0.8945 (m-10) cc_final: 0.8642 (m-10) REVERT: H 46 GLU cc_start: 0.8177 (mp0) cc_final: 0.7950 (mp0) REVERT: L 70 ASP cc_start: 0.8507 (m-30) cc_final: 0.8037 (p0) REVERT: G 102 TYR cc_start: 0.8879 (m-80) cc_final: 0.8578 (m-10) REVERT: D 150 MET cc_start: 0.8798 (mmm) cc_final: 0.8504 (mmt) REVERT: F 545 LEU cc_start: 0.8971 (mt) cc_final: 0.8732 (tp) REVERT: F 571 TRP cc_start: 0.8621 (m-90) cc_final: 0.8396 (m-90) REVERT: F 656 ASN cc_start: 0.9434 (m-40) cc_final: 0.9169 (m-40) REVERT: K 49 TYR cc_start: 0.9035 (p90) cc_final: 0.8645 (p90) outliers start: 41 outliers final: 29 residues processed: 226 average time/residue: 0.3109 time to fit residues: 109.7402 Evaluate side-chains 201 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 2.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 355 ASN Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 63 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 185 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 166 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 190 optimal weight: 0.2980 chunk 154 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 114 optimal weight: 0.8980 chunk 200 optimal weight: 9.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.4188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20205 Z= 0.217 Angle : 0.646 9.070 27453 Z= 0.319 Chirality : 0.044 0.331 3354 Planarity : 0.003 0.048 3366 Dihedral : 6.538 48.268 4332 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.43 % Allowed : 6.08 % Favored : 93.49 % Rotamer: Outliers : 1.82 % Allowed : 10.04 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.17), residues: 2334 helix: 0.79 (0.26), residues: 462 sheet: 0.52 (0.20), residues: 666 loop : -0.84 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 427 HIS 0.003 0.001 HIS F 564 PHE 0.014 0.001 PHE G 78 TYR 0.031 0.002 TYR B 643 ARG 0.007 0.000 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 184 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 TRP cc_start: 0.8446 (t-100) cc_final: 0.8068 (t-100) REVERT: A 150 MET cc_start: 0.8721 (mmm) cc_final: 0.8386 (mmt) REVERT: A 161 MET cc_start: 0.8194 (tpt) cc_final: 0.7967 (tpt) REVERT: B 596 TRP cc_start: 0.8906 (m-10) cc_final: 0.8538 (m-90) REVERT: L 70 ASP cc_start: 0.8440 (m-30) cc_final: 0.8000 (p0) REVERT: E 530 MET cc_start: 0.8396 (mpp) cc_final: 0.7555 (mmm) REVERT: G 102 TYR cc_start: 0.8900 (m-80) cc_final: 0.8570 (m-10) REVERT: D 150 MET cc_start: 0.8818 (mmm) cc_final: 0.8460 (mmt) REVERT: F 545 LEU cc_start: 0.9124 (mt) cc_final: 0.8883 (tp) REVERT: F 566 LEU cc_start: 0.8937 (mt) cc_final: 0.8731 (pp) REVERT: F 571 TRP cc_start: 0.8671 (m-90) cc_final: 0.8470 (m-90) REVERT: F 596 TRP cc_start: 0.9132 (m-10) cc_final: 0.8866 (m-10) REVERT: F 626 MET cc_start: 0.8455 (mtp) cc_final: 0.8138 (ttt) REVERT: F 656 ASN cc_start: 0.9422 (m-40) cc_final: 0.9133 (m-40) REVERT: K 49 TYR cc_start: 0.9099 (p90) cc_final: 0.8745 (p90) outliers start: 38 outliers final: 33 residues processed: 211 average time/residue: 0.3199 time to fit residues: 105.5624 Evaluate side-chains 198 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 165 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 355 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 339 ASN Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 568 LEU Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 75 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 131 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 chunk 223 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 73 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 425 ASN H 3 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 89 GLN J 37 GLN ** J 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.4807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.131 20205 Z= 0.586 Angle : 0.864 8.840 27453 Z= 0.432 Chirality : 0.049 0.327 3354 Planarity : 0.006 0.110 3366 Dihedral : 7.568 59.222 4332 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.73 % Allowed : 6.77 % Favored : 92.50 % Rotamer: Outliers : 2.53 % Allowed : 10.52 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.17), residues: 2334 helix: 0.22 (0.24), residues: 465 sheet: 0.32 (0.20), residues: 651 loop : -1.23 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 596 HIS 0.012 0.003 HIS C 352 PHE 0.021 0.003 PHE G 78 TYR 0.041 0.003 TYR B 643 ARG 0.012 0.001 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 147 time to evaluate : 2.343 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: A 150 MET cc_start: 0.8807 (mmm) cc_final: 0.8359 (mmt) REVERT: C 100 MET cc_start: 0.8565 (mtm) cc_final: 0.8335 (mtm) REVERT: C 426 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7688 (mtp) REVERT: E 530 MET cc_start: 0.8743 (mpp) cc_final: 0.8293 (mmm) REVERT: D 150 MET cc_start: 0.9035 (mmm) cc_final: 0.8478 (mmt) REVERT: F 566 LEU cc_start: 0.8908 (mt) cc_final: 0.8669 (pp) REVERT: F 571 TRP cc_start: 0.8863 (m-90) cc_final: 0.8629 (m-90) REVERT: F 656 ASN cc_start: 0.9379 (m-40) cc_final: 0.9110 (m110) REVERT: K 49 TYR cc_start: 0.9311 (p90) cc_final: 0.8979 (p90) outliers start: 53 outliers final: 38 residues processed: 183 average time/residue: 0.3179 time to fit residues: 91.0639 Evaluate side-chains 174 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 135 time to evaluate : 2.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 32 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 426 MET Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 32 ASP Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain J residue 93 ASN Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 125 LEU Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 72 THR Chi-restraints excluded: chain K residue 93 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 215 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 188 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 222 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 102 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20205 Z= 0.202 Angle : 0.658 10.228 27453 Z= 0.327 Chirality : 0.044 0.309 3354 Planarity : 0.004 0.057 3366 Dihedral : 6.632 59.089 4326 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.91 % Favored : 93.44 % Rotamer: Outliers : 1.67 % Allowed : 12.10 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.17), residues: 2334 helix: 0.59 (0.25), residues: 468 sheet: 0.43 (0.20), residues: 690 loop : -1.23 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP E 596 HIS 0.003 0.001 HIS F 564 PHE 0.013 0.001 PHE G 78 TYR 0.042 0.002 TYR B 643 ARG 0.015 0.001 ARG G 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 164 time to evaluate : 2.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8771 (mmm) cc_final: 0.8392 (mmt) REVERT: B 574 LYS cc_start: 0.9335 (mtmm) cc_final: 0.9131 (mtmm) REVERT: B 596 TRP cc_start: 0.8685 (m-10) cc_final: 0.8455 (m-90) REVERT: C 100 MET cc_start: 0.8179 (mtm) cc_final: 0.7943 (mtm) REVERT: C 104 MET cc_start: 0.8791 (tmm) cc_final: 0.8560 (tmm) REVERT: E 530 MET cc_start: 0.8253 (mpp) cc_final: 0.7991 (mmm) REVERT: E 626 MET cc_start: 0.8695 (mtp) cc_final: 0.8299 (ttt) REVERT: E 643 TYR cc_start: 0.8937 (m-80) cc_final: 0.8582 (m-80) REVERT: G 102 TYR cc_start: 0.8947 (m-80) cc_final: 0.8605 (m-10) REVERT: D 150 MET cc_start: 0.8894 (mmm) cc_final: 0.8536 (mmt) REVERT: F 566 LEU cc_start: 0.8918 (mt) cc_final: 0.8707 (pp) REVERT: F 571 TRP cc_start: 0.8667 (m-90) cc_final: 0.8365 (m-90) REVERT: F 656 ASN cc_start: 0.9397 (m-40) cc_final: 0.9111 (m-40) REVERT: I 102 TYR cc_start: 0.8941 (m-10) cc_final: 0.8726 (m-10) REVERT: K 49 TYR cc_start: 0.9150 (p90) cc_final: 0.8879 (p90) outliers start: 35 outliers final: 26 residues processed: 188 average time/residue: 0.3194 time to fit residues: 93.1250 Evaluate side-chains 176 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 133 ASN Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 133 ASN Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 137 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 132 optimal weight: 7.9990 chunk 67 optimal weight: 9.9990 chunk 43 optimal weight: 0.7980 chunk 141 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 110 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 175 optimal weight: 9.9990 chunk 202 optimal weight: 1.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 20205 Z= 0.264 Angle : 0.657 11.004 27453 Z= 0.327 Chirality : 0.044 0.306 3354 Planarity : 0.004 0.070 3366 Dihedral : 6.192 54.002 4326 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.77 % Allowed : 6.30 % Favored : 92.93 % Rotamer: Outliers : 1.58 % Allowed : 12.63 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.17), residues: 2334 helix: 0.56 (0.25), residues: 468 sheet: 0.44 (0.20), residues: 681 loop : -1.29 (0.18), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 596 HIS 0.004 0.001 HIS A 352 PHE 0.013 0.002 PHE H 78 TYR 0.038 0.002 TYR B 643 ARG 0.013 0.001 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 154 time to evaluate : 2.287 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: A 150 MET cc_start: 0.8783 (mmm) cc_final: 0.8392 (mmt) REVERT: B 643 TYR cc_start: 0.8964 (m-80) cc_final: 0.8724 (m-80) REVERT: C 100 MET cc_start: 0.8230 (mtm) cc_final: 0.7968 (mtm) REVERT: C 104 MET cc_start: 0.8844 (tmm) cc_final: 0.8617 (tmm) REVERT: E 530 MET cc_start: 0.8291 (mpp) cc_final: 0.8078 (mmm) REVERT: E 574 LYS cc_start: 0.9297 (mtmm) cc_final: 0.9063 (ptpp) REVERT: E 626 MET cc_start: 0.8736 (mtp) cc_final: 0.8295 (ttt) REVERT: E 643 TYR cc_start: 0.8937 (m-10) cc_final: 0.8696 (m-80) REVERT: D 150 MET cc_start: 0.8901 (mmm) cc_final: 0.8550 (mmt) REVERT: F 571 TRP cc_start: 0.8739 (m-90) cc_final: 0.8425 (m-90) REVERT: F 656 ASN cc_start: 0.9394 (m-40) cc_final: 0.9113 (m-40) REVERT: I 72 ASP cc_start: 0.7545 (t0) cc_final: 0.7292 (t0) REVERT: I 75 LYS cc_start: 0.9524 (mmmt) cc_final: 0.9281 (mmmt) REVERT: K 49 TYR cc_start: 0.9216 (p90) cc_final: 0.8897 (p90) outliers start: 33 outliers final: 26 residues processed: 177 average time/residue: 0.3267 time to fit residues: 89.9490 Evaluate side-chains 171 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 145 time to evaluate : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 82 ASP Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain I residue 11 VAL Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 213 optimal weight: 0.8980 chunk 194 optimal weight: 3.9990 chunk 207 optimal weight: 9.9990 chunk 124 optimal weight: 0.3980 chunk 90 optimal weight: 5.9990 chunk 162 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 187 optimal weight: 0.7980 chunk 196 optimal weight: 1.9990 chunk 206 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.5221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20205 Z= 0.174 Angle : 0.638 11.764 27453 Z= 0.313 Chirality : 0.044 0.294 3354 Planarity : 0.004 0.073 3366 Dihedral : 5.717 53.280 4326 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.81 % Allowed : 5.61 % Favored : 93.57 % Rotamer: Outliers : 1.53 % Allowed : 12.67 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.17), residues: 2334 helix: 0.76 (0.25), residues: 450 sheet: 0.59 (0.21), residues: 654 loop : -1.27 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 596 HIS 0.003 0.001 HIS F 564 PHE 0.012 0.001 PHE H 78 TYR 0.026 0.002 TYR B 643 ARG 0.014 0.001 ARG H 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 160 time to evaluate : 2.264 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: A 104 MET cc_start: 0.9105 (ppp) cc_final: 0.8832 (tmm) REVERT: A 150 MET cc_start: 0.8759 (mmm) cc_final: 0.8411 (mmt) REVERT: B 530 MET cc_start: 0.6777 (mmm) cc_final: 0.6369 (mmm) REVERT: B 574 LYS cc_start: 0.9441 (mtmm) cc_final: 0.9064 (mtmm) REVERT: C 100 MET cc_start: 0.8103 (mtm) cc_final: 0.7858 (mtm) REVERT: C 104 MET cc_start: 0.8747 (tmm) cc_final: 0.8514 (tmm) REVERT: E 530 MET cc_start: 0.8137 (mpp) cc_final: 0.7798 (mmm) REVERT: E 596 TRP cc_start: 0.8907 (m-10) cc_final: 0.8275 (m-90) REVERT: E 626 MET cc_start: 0.8681 (mtp) cc_final: 0.8239 (ttt) REVERT: G 102 TYR cc_start: 0.8939 (m-80) cc_final: 0.8611 (m-10) REVERT: D 150 MET cc_start: 0.8775 (mmm) cc_final: 0.8571 (mmt) REVERT: F 571 TRP cc_start: 0.8682 (m-90) cc_final: 0.8431 (m-90) REVERT: F 574 LYS cc_start: 0.9220 (mtmm) cc_final: 0.8944 (pttm) REVERT: F 584 GLU cc_start: 0.8494 (tm-30) cc_final: 0.8276 (tm-30) REVERT: F 596 TRP cc_start: 0.8916 (m-10) cc_final: 0.7536 (m-10) REVERT: F 643 TYR cc_start: 0.8933 (m-10) cc_final: 0.8632 (m-80) REVERT: F 656 ASN cc_start: 0.9380 (m-40) cc_final: 0.9077 (m-40) REVERT: I 72 ASP cc_start: 0.7510 (t0) cc_final: 0.7231 (t0) REVERT: I 75 LYS cc_start: 0.9514 (mmmt) cc_final: 0.9270 (mmmt) REVERT: K 49 TYR cc_start: 0.9176 (p90) cc_final: 0.8913 (p90) outliers start: 32 outliers final: 26 residues processed: 181 average time/residue: 0.3288 time to fit residues: 92.8310 Evaluate side-chains 176 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 150 time to evaluate : 2.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 539 VAL Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 219 optimal weight: 10.0000 chunk 133 optimal weight: 9.9990 chunk 104 optimal weight: 9.9990 chunk 152 optimal weight: 8.9990 chunk 230 optimal weight: 0.9980 chunk 211 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 19 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 112 optimal weight: 0.9990 chunk 145 optimal weight: 0.9980 overall best weight: 3.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 20205 Z= 0.345 Angle : 0.705 11.957 27453 Z= 0.350 Chirality : 0.045 0.304 3354 Planarity : 0.005 0.086 3366 Dihedral : 5.964 48.873 4326 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.86 % Allowed : 6.51 % Favored : 92.63 % Rotamer: Outliers : 1.63 % Allowed : 12.67 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.17), residues: 2334 helix: 0.54 (0.25), residues: 450 sheet: 0.43 (0.20), residues: 690 loop : -1.33 (0.18), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP E 596 HIS 0.005 0.001 HIS A 352 PHE 0.014 0.002 PHE G 78 TYR 0.049 0.002 TYR E 643 ARG 0.014 0.001 ARG H 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4668 Ramachandran restraints generated. 2334 Oldfield, 0 Emsley, 2334 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 2.159 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: A 150 MET cc_start: 0.8790 (mmm) cc_final: 0.8400 (mmt) REVERT: B 530 MET cc_start: 0.7107 (mmm) cc_final: 0.6773 (mmm) REVERT: B 574 LYS cc_start: 0.9439 (mtmm) cc_final: 0.9189 (mtmm) REVERT: C 100 MET cc_start: 0.8332 (mtm) cc_final: 0.8073 (mtm) REVERT: C 104 MET cc_start: 0.8898 (tmm) cc_final: 0.8674 (tmm) REVERT: C 426 MET cc_start: 0.8362 (mtm) cc_final: 0.8082 (mtp) REVERT: E 596 TRP cc_start: 0.8905 (m-10) cc_final: 0.8393 (m-90) REVERT: E 626 MET cc_start: 0.8691 (mtp) cc_final: 0.8172 (ttt) REVERT: E 643 TYR cc_start: 0.8929 (m-80) cc_final: 0.8546 (m-80) REVERT: J 42 LYS cc_start: 0.8735 (tptt) cc_final: 0.8475 (tptp) REVERT: D 104 MET cc_start: 0.9169 (ttm) cc_final: 0.8909 (ttm) REVERT: D 150 MET cc_start: 0.8866 (mmm) cc_final: 0.8521 (mmt) REVERT: F 571 TRP cc_start: 0.8750 (m-90) cc_final: 0.8424 (m-90) REVERT: F 656 ASN cc_start: 0.9358 (m-40) cc_final: 0.9066 (m-40) REVERT: I 45 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8837 (mt) REVERT: I 72 ASP cc_start: 0.7565 (t0) cc_final: 0.7304 (t0) REVERT: I 75 LYS cc_start: 0.9540 (mmmt) cc_final: 0.9313 (mmmt) outliers start: 34 outliers final: 27 residues processed: 169 average time/residue: 0.3204 time to fit residues: 84.1771 Evaluate side-chains 168 residues out of total 2091 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 2.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 467 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 616 ASN Chi-restraints excluded: chain H residue 45 LEU Chi-restraints excluded: chain L residue 82 ASP Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 467 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain E residue 539 VAL Chi-restraints excluded: chain E residue 595 ILE Chi-restraints excluded: chain E residue 616 ASN Chi-restraints excluded: chain G residue 45 LEU Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain G residue 80 LEU Chi-restraints excluded: chain D residue 53 PHE Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain D residue 467 THR Chi-restraints excluded: chain F residue 539 VAL Chi-restraints excluded: chain F residue 616 ASN Chi-restraints excluded: chain I residue 45 LEU Chi-restraints excluded: chain K residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 231 random chunks: chunk 195 optimal weight: 0.9980 chunk 56 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 50 optimal weight: 0.0270 chunk 183 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.054710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.043358 restraints weight = 104973.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.045019 restraints weight = 52798.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.046134 restraints weight = 34492.187| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.5450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20205 Z= 0.191 Angle : 0.673 12.634 27453 Z= 0.330 Chirality : 0.044 0.291 3354 Planarity : 0.004 0.064 3366 Dihedral : 5.678 50.112 4326 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.86 % Allowed : 5.70 % Favored : 93.44 % Rotamer: Outliers : 1.34 % Allowed : 13.01 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.17), residues: 2334 helix: 0.63 (0.25), residues: 450 sheet: 0.57 (0.20), residues: 684 loop : -1.30 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 596 HIS 0.003 0.001 HIS D 374 PHE 0.013 0.001 PHE C 383 TYR 0.045 0.002 TYR B 643 ARG 0.013 0.001 ARG G 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3296.57 seconds wall clock time: 62 minutes 11.43 seconds (3731.43 seconds total)