Starting phenix.real_space_refine on Sun Feb 18 00:35:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vkn_21227/02_2024/6vkn_21227.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vkn_21227/02_2024/6vkn_21227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vkn_21227/02_2024/6vkn_21227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vkn_21227/02_2024/6vkn_21227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vkn_21227/02_2024/6vkn_21227.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vkn_21227/02_2024/6vkn_21227.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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 120 5.16 5 C 12636 2.51 5 N 3384 2.21 5 O 4080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L GLU 105": "OE1" <-> "OE2" Residue "H TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 105": "OE1" <-> "OE2" Residue "G TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 105": "OE1" <-> "OE2" Residue "I TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 20220 Number of models: 1 Model: "" Number of chains: 42 Chain: "A" Number of atoms: 3475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3475 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Chain: "B" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1057 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "L" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 818 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "C" Number of atoms: 3475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3475 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Chain: "E" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1057 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "J" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 818 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 97} Chain: "G" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "D" Number of atoms: 3475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3475 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 20, 'TRANS': 420} Chain breaks: 3 Chain: "F" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 1057 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 1, 'TRANS': 130} Chain breaks: 1 Chain: "K" Number of atoms: 818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 818 Classifications: {'peptide': 105} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 97} Chain: "I" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 930 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 5, 'TRANS': 114} Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Y" Number of atoms: 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: "Z" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "a" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "b" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "c" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "d" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "e" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "f" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "g" Number of atoms: 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: "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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "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: "A" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 168 Unusual residues: {'NAG': 12} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 12 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 10.30, per 1000 atoms: 0.51 Number of scatterers: 20220 At special positions: 0 Unit cell: (126.69, 124.63, 154.5, 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 120 16.00 O 4080 8.00 N 3384 7.00 C 12636 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 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=2.02 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=2.03 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=2.15 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 B 598 " - pdb=" SG CYS B 604 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 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=2.02 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=2.03 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=2.15 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 E 598 " - pdb=" SG CYS E 604 " distance=2.03 Simple disulfide: pdb=" SG CYS J 23 " - pdb=" SG CYS J 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 22 " - pdb=" SG CYS G 92 " distance=2.03 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=2.02 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=2.03 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=2.15 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 F 598 " - pdb=" SG CYS F 604 " distance=2.03 Simple disulfide: pdb=" SG CYS K 23 " - pdb=" SG CYS K 88 " distance=2.04 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 92 " 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 Y 4 " - " MAN Y 5 " " MAN g 4 " - " MAN g 5 " ALPHA1-3 " BMA Q 3 " - " MAN Q 4 " " BMA Y 3 " - " MAN Y 4 " " BMA g 3 " - " MAN g 4 " ALPHA1-6 " BMA Q 3 " - " MAN Q 6 " " BMA Y 3 " - " MAN Y 6 " " BMA g 3 " - " MAN g 6 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG 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 X 1 " - " NAG X 2 " " NAG Y 1 " - " NAG Y 2 " " NAG Y 2 " - " BMA Y 3 " " NAG Z 1 " - " NAG Z 2 " " NAG a 1 " - " NAG a 2 " " NAG b 1 " - " NAG b 2 " " NAG c 1 " - " NAG c 2 " " NAG d 1 " - " NAG d 2 " " NAG e 1 " - " NAG e 2 " " NAG f 1 " - " NAG f 2 " " NAG g 1 " - " NAG g 2 " " NAG g 2 " - " BMA g 3 " " NAG h 1 " - " NAG h 2 " " NAG i 1 " - " NAG i 2 " " NAG j 1 " - " NAG j 2 " BETA1-6 " NAG S 1 " - " FUC S 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG a 1 " - " FUC a 3 " " NAG i 1 " - " FUC i 3 " NAG-ASN " NAG A 603 " - " ASN A 234 " " NAG A 608 " - " ASN A 392 " " NAG A 611 " - " ASN A 339 " " NAG A 612 " - " ASN A 332 " " NAG A 613 " - " ASN A 295 " " NAG A 614 " - " ASN A 448 " " NAG A 621 " - " ASN A 301 " " NAG A 624 " - " ASN A 160 " " NAG A 625 " - " ASN A 197 " " NAG A 626 " - " ASN A 133 " " NAG A 627 " - " ASN A 355 " " NAG A 628 " - " ASN A 289 " " NAG B 704 " - " ASN B 618 " " NAG C 603 " - " ASN C 234 " " NAG C 608 " - " ASN C 392 " " NAG C 611 " - " ASN C 339 " " NAG C 612 " - " ASN C 332 " " NAG C 613 " - " ASN C 295 " " NAG C 614 " - " ASN C 448 " " NAG C 621 " - " ASN C 301 " " NAG C 624 " - " ASN C 160 " " NAG C 625 " - " ASN C 197 " " NAG C 626 " - " ASN C 133 " " NAG C 627 " - " ASN C 355 " " NAG C 628 " - " ASN C 289 " " NAG D 603 " - " ASN D 234 " " NAG D 608 " - " ASN D 392 " " NAG D 611 " - " ASN D 339 " " NAG D 612 " - " ASN D 332 " " NAG D 613 " - " ASN D 295 " " NAG D 614 " - " ASN D 448 " " NAG D 621 " - " ASN D 301 " " NAG D 624 " - " ASN D 160 " " NAG D 625 " - " ASN D 197 " " NAG D 626 " - " ASN D 133 " " NAG D 627 " - " ASN D 355 " " NAG D 628 " - " ASN D 289 " " NAG E 704 " - " ASN E 618 " " NAG F 704 " - " ASN F 618 " " NAG M 1 " - " ASN A 88 " " NAG N 1 " - " ASN A 241 " " NAG O 1 " - " ASN A 276 " " NAG P 1 " - " ASN A 386 " " NAG Q 1 " - " ASN A 262 " " NAG R 1 " - " ASN A 156 " " NAG S 1 " - " ASN B 611 " " NAG T 1 " - " ASN B 637 " " NAG U 1 " - " ASN C 88 " " NAG V 1 " - " ASN C 241 " " NAG W 1 " - " ASN C 276 " " NAG X 1 " - " ASN C 386 " " NAG Y 1 " - " ASN C 262 " " NAG Z 1 " - " ASN C 156 " " NAG a 1 " - " ASN E 611 " " NAG b 1 " - " ASN E 637 " " NAG c 1 " - " ASN D 88 " " NAG d 1 " - " ASN D 241 " " NAG e 1 " - " ASN D 276 " " NAG f 1 " - " ASN D 386 " " NAG g 1 " - " ASN D 262 " " NAG h 1 " - " ASN D 156 " " NAG i 1 " - " ASN F 611 " " NAG j 1 " - " ASN F 637 " Time building additional restraints: 8.54 Conformation dependent library (CDL) restraints added in 3.1 seconds 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4452 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 48 sheets defined 22.6% alpha, 50.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.65 Creating SS restraints... Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.534A pdb=" N THR A 71 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 116 removed outlier: 4.102A pdb=" N GLU A 102 " --> pdb=" O ASN A 98 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU A 116 " --> pdb=" O TRP A 112 " (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 334 through 351 removed outlier: 5.332A pdb=" N GLU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLY A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 474 through 479 Processing helix chain 'A' and resid 482 through 484 No H-bonds generated for 'chain 'A' and resid 482 through 484' Processing helix chain 'B' and resid 523 through 528 removed outlier: 4.499A pdb=" N GLY B 527 " --> pdb=" O GLY B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 535 Processing helix chain 'B' and resid 536 through 542 Processing helix chain 'B' and resid 563 through 568 Processing helix chain 'B' and resid 570 through 596 Processing helix chain 'B' and resid 611 through 615 Processing helix chain 'B' and resid 618 through 622 Processing helix chain 'B' and resid 627 through 636 Processing helix chain 'B' and resid 638 through 656 Processing helix chain 'B' and resid 657 through 659 No H-bonds generated for 'chain 'B' and resid 657 through 659' Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.534A pdb=" N THR C 71 " --> pdb=" O ASN C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 116 removed outlier: 4.101A pdb=" N GLU C 102 " --> pdb=" O ASN C 98 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU C 116 " --> pdb=" O TRP C 112 " (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 334 through 351 removed outlier: 5.331A pdb=" N GLU C 340 " --> pdb=" O ALA C 336 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLY C 343 " --> pdb=" O ASN C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 474 through 479 Processing helix chain 'C' and resid 482 through 484 No H-bonds generated for 'chain 'C' and resid 482 through 484' Processing helix chain 'E' and resid 523 through 528 removed outlier: 4.499A pdb=" N GLY E 527 " --> pdb=" O GLY E 524 " (cutoff:3.500A) Processing helix chain 'E' and resid 531 through 535 Processing helix chain 'E' and resid 536 through 542 Processing helix chain 'E' and resid 563 through 568 Processing helix chain 'E' and resid 570 through 596 Processing helix chain 'E' and resid 611 through 615 Processing helix chain 'E' and resid 618 through 622 Processing helix chain 'E' and resid 627 through 636 Processing helix chain 'E' and resid 638 through 656 Processing helix chain 'E' and resid 657 through 659 No H-bonds generated for 'chain 'E' and resid 657 through 659' Processing helix chain 'J' and resid 79 through 83 Processing helix chain 'G' and resid 61 through 64 Processing helix chain 'G' and resid 83 through 87 Processing helix chain 'D' and resid 67 through 72 removed outlier: 3.534A pdb=" N THR D 71 " --> pdb=" O ASN D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 116 removed outlier: 4.101A pdb=" N GLU D 102 " --> pdb=" O ASN D 98 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU D 116 " --> pdb=" O TRP D 112 " (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 334 through 351 removed outlier: 5.331A pdb=" N GLU D 340 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLY D 343 " --> pdb=" O ASN D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 474 through 479 Processing helix chain 'D' and resid 482 through 484 No H-bonds generated for 'chain 'D' and resid 482 through 484' Processing helix chain 'F' and resid 523 through 528 removed outlier: 4.499A pdb=" N GLY F 527 " --> pdb=" O GLY F 524 " (cutoff:3.500A) Processing helix chain 'F' and resid 531 through 535 Processing helix chain 'F' and resid 536 through 542 Processing helix chain 'F' and resid 563 through 568 Processing helix chain 'F' and resid 570 through 596 Processing helix chain 'F' and resid 611 through 615 Processing helix chain 'F' and resid 618 through 622 Processing helix chain 'F' and resid 627 through 636 Processing helix chain 'F' and resid 638 through 656 Processing helix chain 'F' and resid 657 through 659 No H-bonds generated for 'chain 'F' and resid 657 through 659' Processing helix chain 'K' and resid 79 through 83 Processing helix chain 'I' and resid 61 through 64 Processing helix chain 'I' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 494 through 497 Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 47 removed outlier: 3.548A pdb=" N ILE A 225 " --> pdb=" O VAL A 245 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AA4, first strand: chain 'A' and resid 91 through 94 Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 177 Processing sheet with id=AA6, first strand: chain 'A' and resid 200 through 203 removed outlier: 6.329A pdb=" N ALA A 200 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N TYR A 435 " --> pdb=" O ALA A 200 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR A 202 " --> pdb=" O TYR A 435 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.709A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.880A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.878A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.891A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE A 382 " --> pdb=" O LYS A 421 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 271 through 274 removed outlier: 10.891A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 11.878A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 11.880A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE A 358 " --> pdb=" O GLU A 466 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N PHE A 468 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG A 360 " --> pdb=" O PHE A 468 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 259 through 261 removed outlier: 5.709A pdb=" N GLY A 441 " --> pdb=" O ASN A 300 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASN A 300 " --> pdb=" O GLY A 441 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY A 451 " --> pdb=" O GLU A 290 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N GLU A 290 " --> pdb=" O GLY A 451 " (cutoff:3.500A) removed outlier: 11.880A pdb=" N ILE A 453 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 11.878A pdb=" N LEU A 288 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR A 455 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 10.891A pdb=" N VAL A 286 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 271 through 274 removed outlier: 6.762A pdb=" N ASN A 301 " --> pdb=" O ILE A 323 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE A 323 " --> pdb=" O ASN A 301 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N THR A 303 " --> pdb=" O GLY A 321 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N GLN A 315 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.614A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.417A pdb=" N TRP H 35 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N TYR H 50 " --> pdb=" O TRP H 35 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AB8, first strand: chain 'C' and resid 494 through 497 Processing sheet with id=AB9, first strand: chain 'C' and resid 45 through 47 removed outlier: 3.547A pdb=" N ILE C 225 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 53 through 55 Processing sheet with id=AC2, first strand: chain 'C' and resid 91 through 94 Processing sheet with id=AC3, first strand: chain 'C' and resid 169 through 177 Processing sheet with id=AC4, first strand: chain 'C' and resid 200 through 203 removed outlier: 6.329A pdb=" N ALA C 200 " --> pdb=" O ALA C 433 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N TYR C 435 " --> pdb=" O ALA C 200 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR C 202 " --> pdb=" O TYR C 435 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 259 through 261 removed outlier: 5.709A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.880A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.879A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.892A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE C 382 " --> pdb=" O LYS C 421 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 271 through 274 removed outlier: 10.892A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 11.879A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 11.880A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE C 358 " --> pdb=" O GLU C 466 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N PHE C 468 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG C 360 " --> pdb=" O PHE C 468 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 259 through 261 removed outlier: 5.709A pdb=" N GLY C 441 " --> pdb=" O ASN C 300 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ASN C 300 " --> pdb=" O GLY C 441 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY C 451 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N GLU C 290 " --> pdb=" O GLY C 451 " (cutoff:3.500A) removed outlier: 11.880A pdb=" N ILE C 453 " --> pdb=" O LEU C 288 " (cutoff:3.500A) removed outlier: 11.879A pdb=" N LEU C 288 " --> pdb=" O ILE C 453 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR C 455 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 10.892A pdb=" N VAL C 286 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 271 through 274 removed outlier: 6.762A pdb=" N ASN C 301 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE C 323 " --> pdb=" O ASN C 301 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N THR C 303 " --> pdb=" O GLY C 321 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN C 315 " --> pdb=" O ILE C 309 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'J' and resid 4 through 7 Processing sheet with id=AD1, first strand: chain 'J' and resid 10 through 13 removed outlier: 6.614A pdb=" N LEU J 33 " --> pdb=" O TYR J 49 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR J 49 " --> pdb=" O LEU J 33 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N TRP J 35 " --> pdb=" O LEU J 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 10 through 13 Processing sheet with id=AD3, first strand: chain 'G' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'G' and resid 11 through 12 removed outlier: 6.417A pdb=" N TRP G 35 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR G 50 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 11 through 12 Processing sheet with id=AD6, first strand: chain 'D' and resid 494 through 497 Processing sheet with id=AD7, first strand: chain 'D' and resid 45 through 47 removed outlier: 3.549A pdb=" N ILE D 225 " --> pdb=" O VAL D 245 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 53 through 55 Processing sheet with id=AD9, first strand: chain 'D' and resid 91 through 94 Processing sheet with id=AE1, first strand: chain 'D' and resid 169 through 177 Processing sheet with id=AE2, first strand: chain 'D' and resid 200 through 203 removed outlier: 6.329A pdb=" N ALA D 200 " --> pdb=" O ALA D 433 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N TYR D 435 " --> pdb=" O ALA D 200 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR D 202 " --> pdb=" O TYR D 435 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 259 through 261 removed outlier: 5.709A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY D 451 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N GLU D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 11.881A pdb=" N ILE D 453 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 11.878A pdb=" N LEU D 288 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 10.891A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N PHE D 382 " --> pdb=" O LYS D 421 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 271 through 274 removed outlier: 10.891A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 11.878A pdb=" N LEU D 288 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 11.881A pdb=" N ILE D 453 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N GLU D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY D 451 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE D 358 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N PHE D 468 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ARG D 360 " --> pdb=" O PHE D 468 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 259 through 261 removed outlier: 5.709A pdb=" N GLY D 441 " --> pdb=" O ASN D 300 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N ASN D 300 " --> pdb=" O GLY D 441 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLY D 451 " --> pdb=" O GLU D 290 " (cutoff:3.500A) removed outlier: 10.561A pdb=" N GLU D 290 " --> pdb=" O GLY D 451 " (cutoff:3.500A) removed outlier: 11.881A pdb=" N ILE D 453 " --> pdb=" O LEU D 288 " (cutoff:3.500A) removed outlier: 11.878A pdb=" N LEU D 288 " --> pdb=" O ILE D 453 " (cutoff:3.500A) removed outlier: 10.763A pdb=" N THR D 455 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 10.891A pdb=" N VAL D 286 " --> pdb=" O THR D 455 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 271 through 274 removed outlier: 6.762A pdb=" N ASN D 301 " --> pdb=" O ILE D 323 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE D 323 " --> pdb=" O ASN D 301 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N THR D 303 " --> pdb=" O GLY D 321 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN D 315 " --> pdb=" O ILE D 309 " (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: 6.615A pdb=" N LEU K 33 " --> pdb=" O TYR K 49 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR K 49 " --> pdb=" O LEU K 33 " (cutoff:3.500A) removed outlier: 6.632A 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 Processing sheet with id=AF1, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AF2, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.417A pdb=" N TRP I 35 " --> pdb=" O TYR I 50 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N TYR I 50 " --> pdb=" O TRP I 35 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'I' and resid 11 through 12 903 hydrogen bonds defined for protein. 2241 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: 7.53 Time building geometry restraints manager: 9.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3327 1.31 - 1.44: 5476 1.44 - 1.56: 11597 1.56 - 1.69: 69 1.69 - 1.82: 153 Bond restraints: 20622 Sorted by residual: bond pdb=" NE1 TRP F 623 " pdb=" CE2 TRP F 623 " ideal model delta sigma weight residual 1.370 1.317 0.053 1.10e-02 8.26e+03 2.32e+01 bond pdb=" NE1 TRP B 623 " pdb=" CE2 TRP B 623 " ideal model delta sigma weight residual 1.370 1.317 0.053 1.10e-02 8.26e+03 2.29e+01 bond pdb=" NE1 TRP E 623 " pdb=" CE2 TRP E 623 " ideal model delta sigma weight residual 1.370 1.318 0.052 1.10e-02 8.26e+03 2.26e+01 bond pdb=" CB TYR A 484 " pdb=" CG TYR A 484 " ideal model delta sigma weight residual 1.512 1.414 0.098 2.20e-02 2.07e+03 2.00e+01 bond pdb=" CB TYR C 484 " pdb=" CG TYR C 484 " ideal model delta sigma weight residual 1.512 1.414 0.098 2.20e-02 2.07e+03 2.00e+01 ... (remaining 20617 not shown) Histogram of bond angle deviations from ideal: 94.28 - 102.27: 129 102.27 - 110.27: 6380 110.27 - 118.26: 10370 118.26 - 126.25: 10744 126.25 - 134.24: 388 Bond angle restraints: 28011 Sorted by residual: angle pdb=" N VAL F 570 " pdb=" CA VAL F 570 " pdb=" C VAL F 570 " ideal model delta sigma weight residual 112.12 101.76 10.36 8.40e-01 1.42e+00 1.52e+02 angle pdb=" N VAL B 570 " pdb=" CA VAL B 570 " pdb=" C VAL B 570 " ideal model delta sigma weight residual 112.12 101.78 10.34 8.40e-01 1.42e+00 1.52e+02 angle pdb=" N VAL E 570 " pdb=" CA VAL E 570 " pdb=" C VAL E 570 " ideal model delta sigma weight residual 112.12 101.80 10.32 8.40e-01 1.42e+00 1.51e+02 angle pdb=" N TRP D 35 " pdb=" CA TRP D 35 " pdb=" C TRP D 35 " ideal model delta sigma weight residual 109.54 122.75 -13.21 1.37e+00 5.33e-01 9.30e+01 angle pdb=" N TRP A 35 " pdb=" CA TRP A 35 " pdb=" C TRP A 35 " ideal model delta sigma weight residual 109.54 122.75 -13.21 1.37e+00 5.33e-01 9.30e+01 ... (remaining 28006 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.01: 13140 22.01 - 44.02: 342 44.02 - 66.04: 117 66.04 - 88.05: 36 88.05 - 110.06: 15 Dihedral angle restraints: 13650 sinusoidal: 6759 harmonic: 6891 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 93.00 152.47 -59.47 1 1.00e+01 1.00e-02 4.72e+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 93.00 152.45 -59.45 1 1.00e+01 1.00e-02 4.72e+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 93.00 152.45 -59.45 1 1.00e+01 1.00e-02 4.72e+01 ... (remaining 13647 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 2661 0.111 - 0.223: 700 0.223 - 0.334: 77 0.334 - 0.445: 0 0.445 - 0.556: 3 Chirality restraints: 3441 Sorted by residual: chirality pdb=" C1 BMA Y 3 " pdb=" O4 NAG Y 2 " pdb=" C2 BMA Y 3 " pdb=" O5 BMA Y 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.15e+01 chirality pdb=" C1 BMA g 3 " pdb=" O4 NAG g 2 " pdb=" C2 BMA g 3 " pdb=" O5 BMA g 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.13e+01 chirality pdb=" C1 BMA Q 3 " pdb=" O4 NAG Q 2 " pdb=" C2 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.57 0.17 2.00e-02 2.50e+03 7.12e+01 ... (remaining 3438 not shown) Planarity restraints: 3492 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 133 " -0.089 2.00e-02 2.50e+03 9.25e-02 1.07e+02 pdb=" CG ASN C 133 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN C 133 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN C 133 " 0.144 2.00e-02 2.50e+03 pdb=" C1 NAG C 626 " -0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 133 " 0.089 2.00e-02 2.50e+03 9.25e-02 1.07e+02 pdb=" CG ASN A 133 " -0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN A 133 " -0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN A 133 " -0.144 2.00e-02 2.50e+03 pdb=" C1 NAG A 626 " 0.111 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 133 " -0.089 2.00e-02 2.50e+03 9.23e-02 1.07e+02 pdb=" CG ASN D 133 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASN D 133 " 0.013 2.00e-02 2.50e+03 pdb=" ND2 ASN D 133 " 0.144 2.00e-02 2.50e+03 pdb=" C1 NAG D 626 " -0.110 2.00e-02 2.50e+03 ... (remaining 3489 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5168 2.80 - 3.32: 17101 3.32 - 3.85: 33162 3.85 - 4.37: 38123 4.37 - 4.90: 64124 Nonbonded interactions: 157678 Sorted by model distance: nonbonded pdb=" O GLY F 521 " pdb=" N LEU F 523 " model vdw 2.274 2.520 nonbonded pdb=" O GLY E 521 " pdb=" N LEU E 523 " model vdw 2.274 2.520 nonbonded pdb=" O GLY B 521 " pdb=" N LEU B 523 " model vdw 2.274 2.520 nonbonded pdb=" N ASP J 60 " pdb=" OD1 ASP J 60 " model vdw 2.414 2.520 nonbonded pdb=" N ASP L 60 " pdb=" OD1 ASP L 60 " model vdw 2.415 2.520 ... (remaining 157673 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 'N' selection = chain 'O' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'j' } ncs_group { reference = chain 'Q' selection = chain 'Y' selection = chain 'g' } ncs_group { reference = chain 'S' selection = chain 'a' 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.020 Extract box with map and model: 6.340 Check model and map are aligned: 0.290 Set scattering table: 0.190 Process input model: 52.610 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.370 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 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 : 0.019 0.130 20622 Z= 1.210 Angle : 1.769 13.211 28011 Z= 1.133 Chirality : 0.096 0.556 3441 Planarity : 0.009 0.070 3429 Dihedral : 12.054 110.059 9090 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 1.30 Ramachandran Plot: Outliers : 0.77 % Allowed : 3.58 % Favored : 95.65 % Rotamer: Outliers : 0.85 % Allowed : 1.14 % Favored : 98.01 % Cbeta Deviations : 0.13 % 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: 0.87 (0.17), residues: 2346 helix: -0.49 (0.25), residues: 375 sheet: 1.03 (0.18), residues: 702 loop : 0.84 (0.19), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.008 TRP D 96 HIS 0.007 0.002 HIS A 72 PHE 0.035 0.006 PHE A 383 TYR 0.060 0.008 TYR H 91 ARG 0.006 0.001 ARG C 429 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 588 time to evaluate : 2.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.8017 (mmm) cc_final: 0.7527 (mmt) REVERT: B 607 ASN cc_start: 0.8488 (m-40) cc_final: 0.8064 (t0) REVERT: B 652 GLN cc_start: 0.8346 (tp40) cc_final: 0.8079 (tp40) REVERT: L 100 GLN cc_start: 0.7080 (pm20) cc_final: 0.6105 (mp10) REVERT: H 5 VAL cc_start: 0.7430 (t) cc_final: 0.7220 (m) REVERT: C 150 MET cc_start: 0.7918 (mmm) cc_final: 0.7497 (mmt) REVERT: C 309 ILE cc_start: 0.8999 (tt) cc_final: 0.8712 (tt) REVERT: C 360 ARG cc_start: 0.8245 (ttm170) cc_final: 0.8022 (ttp80) REVERT: E 562 GLN cc_start: 0.6152 (mt0) cc_final: 0.5765 (tt0) REVERT: E 652 GLN cc_start: 0.8263 (tp40) cc_final: 0.7823 (tp40) REVERT: J 36 TYR cc_start: 0.9067 (m-80) cc_final: 0.8752 (m-80) REVERT: J 100 GLN cc_start: 0.7352 (pm20) cc_final: 0.6181 (mp10) REVERT: D 150 MET cc_start: 0.8053 (mmm) cc_final: 0.7504 (mmt) REVERT: D 474 ASP cc_start: 0.6025 (t0) cc_final: 0.5816 (t0) REVERT: F 607 ASN cc_start: 0.8489 (m-40) cc_final: 0.8285 (t0) REVERT: F 635 ILE cc_start: 0.9332 (mm) cc_final: 0.9047 (tt) REVERT: F 652 GLN cc_start: 0.8423 (tp40) cc_final: 0.8089 (tp40) REVERT: K 72 THR cc_start: 0.8599 (m) cc_final: 0.8365 (p) REVERT: K 82 ASP cc_start: 0.7846 (m-30) cc_final: 0.7520 (m-30) REVERT: K 100 GLN cc_start: 0.7291 (pm20) cc_final: 0.6275 (mp10) REVERT: I 5 VAL cc_start: 0.7500 (t) cc_final: 0.7278 (m) outliers start: 18 outliers final: 1 residues processed: 597 average time/residue: 0.3570 time to fit residues: 312.0906 Evaluate side-chains 300 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 299 time to evaluate : 2.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 659 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 0.9980 chunk 179 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 121 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 112 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 215 optimal weight: 9.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 478 ASN B 543 ASN C 130 GLN E 607 ASN E 658 GLN J 38 GLN J 92 ASN D 130 GLN D 478 ASN F 543 ASN K 92 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20622 Z= 0.233 Angle : 0.724 9.453 28011 Z= 0.382 Chirality : 0.047 0.177 3441 Planarity : 0.004 0.042 3429 Dihedral : 8.271 57.873 4667 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.62 % Favored : 96.12 % Rotamer: Outliers : 2.89 % Allowed : 8.30 % Favored : 88.81 % 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: 0.72 (0.18), residues: 2346 helix: 0.53 (0.28), residues: 393 sheet: 0.80 (0.18), residues: 807 loop : 0.37 (0.20), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP I 103 HIS 0.004 0.001 HIS C 330 PHE 0.017 0.002 PHE H 78 TYR 0.015 0.001 TYR A 484 ARG 0.006 0.001 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 353 time to evaluate : 2.253 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: 0.7760 (mmm) cc_final: 0.7042 (mmt) REVERT: A 194 ILE cc_start: 0.9402 (tp) cc_final: 0.9170 (tt) REVERT: A 426 MET cc_start: 0.5514 (tpp) cc_final: 0.5045 (mmt) REVERT: B 624 ASP cc_start: 0.8510 (m-30) cc_final: 0.8278 (m-30) REVERT: B 659 ASP cc_start: 0.8574 (t70) cc_final: 0.8234 (t0) REVERT: L 100 GLN cc_start: 0.7187 (pm20) cc_final: 0.6587 (mp10) REVERT: L 104 VAL cc_start: 0.8134 (OUTLIER) cc_final: 0.7924 (t) REVERT: H 68 THR cc_start: 0.7827 (OUTLIER) cc_final: 0.7561 (t) REVERT: H 76 ASN cc_start: 0.6619 (p0) cc_final: 0.6349 (t0) REVERT: C 150 MET cc_start: 0.7719 (mmm) cc_final: 0.7407 (mmt) REVERT: C 194 ILE cc_start: 0.9389 (tp) cc_final: 0.9098 (tt) REVERT: C 360 ARG cc_start: 0.8127 (ttm170) cc_final: 0.7895 (ttp80) REVERT: C 426 MET cc_start: 0.5835 (tpp) cc_final: 0.5349 (mmt) REVERT: E 652 GLN cc_start: 0.8266 (tp40) cc_final: 0.7899 (tp40) REVERT: J 61 ARG cc_start: 0.7680 (mtp180) cc_final: 0.7057 (mtm110) REVERT: J 100 GLN cc_start: 0.7416 (pm20) cc_final: 0.6665 (mp10) REVERT: G 68 THR cc_start: 0.7651 (OUTLIER) cc_final: 0.7378 (t) REVERT: G 76 ASN cc_start: 0.6831 (p0) cc_final: 0.6389 (t0) REVERT: D 150 MET cc_start: 0.7840 (mmm) cc_final: 0.7327 (mmt) REVERT: D 426 MET cc_start: 0.5913 (tpp) cc_final: 0.5486 (mmt) REVERT: F 652 GLN cc_start: 0.8477 (tp40) cc_final: 0.8144 (tp40) REVERT: F 659 ASP cc_start: 0.8495 (t70) cc_final: 0.7319 (p0) REVERT: K 72 THR cc_start: 0.8472 (m) cc_final: 0.8243 (p) REVERT: K 100 GLN cc_start: 0.7366 (pm20) cc_final: 0.6755 (mp10) REVERT: K 104 VAL cc_start: 0.7988 (OUTLIER) cc_final: 0.7682 (t) outliers start: 61 outliers final: 37 residues processed: 386 average time/residue: 0.3043 time to fit residues: 182.6264 Evaluate side-chains 331 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 290 time to evaluate : 2.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 88 ASN Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 450 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain B residue 637 ASN Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 104 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain C residue 57 ASP Chi-restraints excluded: chain C residue 88 ASN Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 637 ASN Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain I residue 37 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 119 optimal weight: 7.9990 chunk 66 optimal weight: 0.0980 chunk 179 optimal weight: 7.9990 chunk 146 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 215 optimal weight: 0.0270 chunk 232 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 chunk 213 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 overall best weight: 2.0244 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 HIS C 374 HIS ** E 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 103 GLN D 374 HIS D 478 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20622 Z= 0.296 Angle : 0.694 8.618 28011 Z= 0.361 Chirality : 0.046 0.186 3441 Planarity : 0.004 0.040 3429 Dihedral : 6.850 40.599 4665 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.65 % Favored : 94.97 % Rotamer: Outliers : 3.94 % Allowed : 9.53 % Favored : 86.53 % 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: 0.43 (0.18), residues: 2346 helix: 0.43 (0.28), residues: 393 sheet: 0.83 (0.18), residues: 762 loop : -0.03 (0.19), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 571 HIS 0.004 0.001 HIS C 330 PHE 0.019 0.002 PHE D 53 TYR 0.024 0.002 TYR I 50 ARG 0.005 0.000 ARG C 456 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 310 time to evaluate : 2.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7852 (mmm) cc_final: 0.7545 (mmt) REVERT: A 426 MET cc_start: 0.5488 (tpp) cc_final: 0.5199 (mmt) REVERT: B 652 GLN cc_start: 0.8591 (tp40) cc_final: 0.8346 (tp40) REVERT: B 659 ASP cc_start: 0.8802 (t70) cc_final: 0.8323 (t0) REVERT: L 29 VAL cc_start: 0.8505 (m) cc_final: 0.8279 (p) REVERT: H 68 THR cc_start: 0.7796 (OUTLIER) cc_final: 0.7493 (t) REVERT: H 81 LYS cc_start: 0.8193 (mttm) cc_final: 0.7938 (mttm) REVERT: C 150 MET cc_start: 0.7875 (mmm) cc_final: 0.7613 (mmt) REVERT: C 360 ARG cc_start: 0.8378 (ttm170) cc_final: 0.8175 (ttp80) REVERT: C 426 MET cc_start: 0.5933 (tpp) cc_final: 0.5645 (mmt) REVERT: E 652 GLN cc_start: 0.8511 (tp40) cc_final: 0.8199 (tp40) REVERT: E 659 ASP cc_start: 0.8589 (t70) cc_final: 0.8113 (t0) REVERT: J 29 VAL cc_start: 0.8384 (m) cc_final: 0.8160 (p) REVERT: J 61 ARG cc_start: 0.7704 (mtp180) cc_final: 0.7194 (mtm110) REVERT: G 68 THR cc_start: 0.7721 (OUTLIER) cc_final: 0.7397 (t) REVERT: D 103 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.7589 (tm130) REVERT: D 150 MET cc_start: 0.7911 (mmm) cc_final: 0.7271 (mmt) REVERT: D 426 MET cc_start: 0.5906 (tpp) cc_final: 0.5554 (mmt) REVERT: F 652 GLN cc_start: 0.8733 (tp40) cc_final: 0.8435 (tp40) REVERT: F 659 ASP cc_start: 0.8775 (t70) cc_final: 0.8300 (t0) REVERT: K 29 VAL cc_start: 0.8538 (m) cc_final: 0.8280 (p) REVERT: K 104 VAL cc_start: 0.7945 (p) cc_final: 0.7641 (t) outliers start: 83 outliers final: 62 residues processed: 356 average time/residue: 0.2953 time to fit residues: 167.0323 Evaluate side-chains 338 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 273 time to evaluate : 2.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 569 THR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain E residue 637 ASN Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 24 VAL Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 567 LYS Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 103 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 213 optimal weight: 1.9990 chunk 162 optimal weight: 0.0060 chunk 111 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 144 optimal weight: 9.9990 chunk 216 optimal weight: 10.0000 chunk 229 optimal weight: 6.9990 chunk 113 optimal weight: 1.9990 chunk 205 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 543 ASN C 478 ASN ** E 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 20622 Z= 0.220 Angle : 0.620 13.173 28011 Z= 0.319 Chirality : 0.044 0.273 3441 Planarity : 0.004 0.041 3429 Dihedral : 6.131 32.397 4665 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.38 % Allowed : 4.01 % Favored : 95.61 % Rotamer: Outliers : 3.22 % Allowed : 12.33 % Favored : 84.45 % 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: 0.29 (0.18), residues: 2346 helix: 0.58 (0.28), residues: 393 sheet: 0.52 (0.18), residues: 798 loop : -0.07 (0.20), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 103 HIS 0.002 0.001 HIS C 330 PHE 0.015 0.002 PHE I 78 TYR 0.017 0.001 TYR I 50 ARG 0.003 0.000 ARG G 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 305 time to evaluate : 2.868 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7876 (mmm) cc_final: 0.7551 (mmt) REVERT: A 426 MET cc_start: 0.5447 (tpp) cc_final: 0.5188 (mmt) REVERT: B 652 GLN cc_start: 0.8693 (tp40) cc_final: 0.8271 (tp40) REVERT: B 659 ASP cc_start: 0.8928 (t70) cc_final: 0.8440 (t0) REVERT: L 81 GLU cc_start: 0.7234 (mp0) cc_final: 0.5412 (tt0) REVERT: H 81 LYS cc_start: 0.8285 (mttm) cc_final: 0.8062 (mttm) REVERT: C 150 MET cc_start: 0.7796 (mmm) cc_final: 0.7548 (mmt) REVERT: C 426 MET cc_start: 0.5788 (tpp) cc_final: 0.5541 (mmt) REVERT: E 652 GLN cc_start: 0.8500 (tp40) cc_final: 0.8224 (tp40) REVERT: E 659 ASP cc_start: 0.8647 (t70) cc_final: 0.8210 (t0) REVERT: J 61 ARG cc_start: 0.7727 (mtp180) cc_final: 0.7273 (mtm110) REVERT: J 104 VAL cc_start: 0.8205 (t) cc_final: 0.7957 (t) REVERT: G 50 TYR cc_start: 0.9038 (p90) cc_final: 0.8744 (p90) REVERT: G 58 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7807 (ttm170) REVERT: D 103 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.7663 (tm-30) REVERT: D 150 MET cc_start: 0.7931 (mmm) cc_final: 0.7323 (mmt) REVERT: D 217 TYR cc_start: 0.9220 (m-80) cc_final: 0.8586 (m-80) REVERT: F 652 GLN cc_start: 0.8683 (tp40) cc_final: 0.8391 (tp40) REVERT: F 659 ASP cc_start: 0.8859 (t70) cc_final: 0.8401 (t0) REVERT: K 29 VAL cc_start: 0.8583 (m) cc_final: 0.8315 (p) REVERT: K 72 THR cc_start: 0.8574 (m) cc_final: 0.8274 (p) REVERT: I 58 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.6720 (ttm-80) outliers start: 68 outliers final: 51 residues processed: 344 average time/residue: 0.3048 time to fit residues: 165.3818 Evaluate side-chains 321 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 267 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 450 THR Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 626 MET Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 103 GLN Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 450 THR Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 567 LYS Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 91 GLU Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain I residue 103 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 190 optimal weight: 5.9990 chunk 130 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 170 optimal weight: 0.4980 chunk 94 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 chunk 158 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 116 optimal weight: 0.9980 chunk 205 optimal weight: 0.3980 chunk 57 optimal weight: 9.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 ASN ** C 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 20622 Z= 0.152 Angle : 0.574 16.128 28011 Z= 0.295 Chirality : 0.043 0.205 3441 Planarity : 0.004 0.040 3429 Dihedral : 5.456 30.833 4665 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.38 % Allowed : 3.79 % Favored : 95.82 % Rotamer: Outliers : 2.89 % Allowed : 13.66 % Favored : 83.45 % 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: 0.36 (0.18), residues: 2346 helix: 0.91 (0.29), residues: 393 sheet: 0.44 (0.17), residues: 834 loop : -0.05 (0.20), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 427 HIS 0.004 0.000 HIS D 105 PHE 0.016 0.001 PHE H 78 TYR 0.017 0.001 TYR I 50 ARG 0.002 0.000 ARG A 419 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 306 time to evaluate : 2.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 150 MET cc_start: 0.7879 (mmm) cc_final: 0.7358 (mmt) REVERT: B 652 GLN cc_start: 0.8664 (tp40) cc_final: 0.8311 (tp40) REVERT: B 659 ASP cc_start: 0.8941 (t70) cc_final: 0.8523 (t0) REVERT: H 51 ILE cc_start: 0.8800 (tt) cc_final: 0.8591 (tt) REVERT: C 95 MET cc_start: 0.8566 (ptm) cc_final: 0.7938 (ttp) REVERT: C 150 MET cc_start: 0.7771 (mmm) cc_final: 0.7519 (mmt) REVERT: C 426 MET cc_start: 0.5530 (tpp) cc_final: 0.5299 (mmt) REVERT: C 484 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.7016 (t80) REVERT: E 652 GLN cc_start: 0.8479 (tp40) cc_final: 0.8062 (tp40) REVERT: E 659 ASP cc_start: 0.8689 (t70) cc_final: 0.8272 (t0) REVERT: J 61 ARG cc_start: 0.7641 (mtp180) cc_final: 0.7279 (mtm110) REVERT: G 51 ILE cc_start: 0.8612 (tt) cc_final: 0.8281 (tt) REVERT: G 58 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7671 (ttm170) REVERT: D 150 MET cc_start: 0.7924 (mmm) cc_final: 0.7337 (mmt) REVERT: D 217 TYR cc_start: 0.9253 (m-80) cc_final: 0.8454 (m-80) REVERT: D 478 ASN cc_start: 0.7848 (t160) cc_final: 0.7577 (t0) REVERT: F 652 GLN cc_start: 0.8715 (tp40) cc_final: 0.8400 (tp40) REVERT: F 659 ASP cc_start: 0.8860 (t70) cc_final: 0.8410 (t0) REVERT: K 4 MET cc_start: 0.7379 (ptp) cc_final: 0.7134 (ptp) REVERT: K 39 LYS cc_start: 0.7947 (mtmm) cc_final: 0.7287 (mtmm) REVERT: K 72 THR cc_start: 0.8515 (m) cc_final: 0.8203 (p) REVERT: K 104 VAL cc_start: 0.7839 (p) cc_final: 0.7569 (t) REVERT: I 51 ILE cc_start: 0.8571 (tt) cc_final: 0.8239 (tt) outliers start: 61 outliers final: 42 residues processed: 341 average time/residue: 0.2836 time to fit residues: 153.9837 Evaluate side-chains 322 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 278 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 620 SER Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 106 ILE Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain D residue 57 ASP Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain I residue 103 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 77 optimal weight: 4.9990 chunk 206 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 120 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 103 GLN ** E 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.4485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 20622 Z= 0.380 Angle : 0.701 13.693 28011 Z= 0.358 Chirality : 0.047 0.204 3441 Planarity : 0.004 0.041 3429 Dihedral : 6.138 52.743 4665 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.12 % Favored : 94.50 % Rotamer: Outliers : 3.89 % Allowed : 13.04 % Favored : 83.07 % 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: 0.01 (0.18), residues: 2346 helix: 0.50 (0.27), residues: 393 sheet: 0.30 (0.17), residues: 795 loop : -0.28 (0.20), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 112 HIS 0.005 0.001 HIS C 105 PHE 0.020 0.002 PHE H 100C TYR 0.016 0.002 TYR H 50 ARG 0.003 0.000 ARG A 503 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 287 time to evaluate : 2.346 Fit side-chains REVERT: A 150 MET cc_start: 0.8018 (mmm) cc_final: 0.7467 (mmt) REVERT: B 652 GLN cc_start: 0.8798 (tp40) cc_final: 0.8381 (tp40) REVERT: B 659 ASP cc_start: 0.9081 (t70) cc_final: 0.8537 (t0) REVERT: L 100 GLN cc_start: 0.7671 (pm20) cc_final: 0.6211 (mp10) REVERT: H 16 GLU cc_start: 0.5641 (mt-10) cc_final: 0.5373 (mt-10) REVERT: C 150 MET cc_start: 0.7961 (mmm) cc_final: 0.7596 (mmt) REVERT: C 426 MET cc_start: 0.5617 (tpp) cc_final: 0.5357 (mmt) REVERT: E 655 LYS cc_start: 0.8826 (mtpp) cc_final: 0.8542 (ttmt) REVERT: J 61 ARG cc_start: 0.7801 (mtp180) cc_final: 0.7399 (mtm110) REVERT: G 58 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7624 (ttm170) REVERT: D 150 MET cc_start: 0.8075 (mmm) cc_final: 0.7477 (mmt) REVERT: F 652 GLN cc_start: 0.8788 (tp40) cc_final: 0.8494 (tp40) REVERT: F 659 ASP cc_start: 0.9013 (t70) cc_final: 0.8496 (t0) REVERT: K 4 MET cc_start: 0.7428 (ptp) cc_final: 0.7178 (ptp) REVERT: K 100 GLN cc_start: 0.7831 (pm20) cc_final: 0.6352 (mp10) REVERT: I 58 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7268 (ttm-80) outliers start: 82 outliers final: 64 residues processed: 334 average time/residue: 0.3021 time to fit residues: 156.2721 Evaluate side-chains 336 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 270 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 115 SER Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 115 SER Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 184 ILE Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain G residue 12 VAL Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain K residue 104 VAL Chi-restraints excluded: chain K residue 106 ILE Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 103 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 221 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 167 optimal weight: 4.9990 chunk 129 optimal weight: 0.8980 chunk 193 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 228 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 105 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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** ** E 625 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20622 Z= 0.183 Angle : 0.587 13.615 28011 Z= 0.302 Chirality : 0.044 0.176 3441 Planarity : 0.004 0.039 3429 Dihedral : 5.864 58.984 4665 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.67 % Favored : 95.91 % Rotamer: Outliers : 3.08 % Allowed : 14.51 % Favored : 82.41 % 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: 0.17 (0.18), residues: 2346 helix: 0.89 (0.28), residues: 393 sheet: 0.36 (0.17), residues: 795 loop : -0.25 (0.20), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 623 HIS 0.003 0.001 HIS C 105 PHE 0.013 0.001 PHE H 100C TYR 0.016 0.001 TYR I 50 ARG 0.003 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 285 time to evaluate : 2.241 Fit side-chains REVERT: A 150 MET cc_start: 0.7910 (mmm) cc_final: 0.7346 (mmt) REVERT: B 652 GLN cc_start: 0.8697 (tp40) cc_final: 0.8381 (tp40) REVERT: B 659 ASP cc_start: 0.8952 (t70) cc_final: 0.8535 (t0) REVERT: H 16 GLU cc_start: 0.5482 (mt-10) cc_final: 0.5263 (mt-10) REVERT: C 95 MET cc_start: 0.8579 (ptm) cc_final: 0.8040 (ttm) REVERT: C 150 MET cc_start: 0.7932 (mmm) cc_final: 0.7632 (mmt) REVERT: C 426 MET cc_start: 0.5385 (tpp) cc_final: 0.5151 (mmt) REVERT: E 655 LYS cc_start: 0.8736 (mtpp) cc_final: 0.8388 (ttmt) REVERT: E 659 ASP cc_start: 0.8858 (t70) cc_final: 0.8368 (t0) REVERT: J 61 ARG cc_start: 0.7684 (mtp180) cc_final: 0.7373 (mtm110) REVERT: G 51 ILE cc_start: 0.8628 (tt) cc_final: 0.8359 (tt) REVERT: G 58 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7648 (ttm170) REVERT: D 150 MET cc_start: 0.8032 (mmm) cc_final: 0.7479 (mmt) REVERT: D 478 ASN cc_start: 0.7910 (t160) cc_final: 0.7667 (t0) REVERT: F 652 GLN cc_start: 0.8762 (tp40) cc_final: 0.8533 (tp40) REVERT: F 659 ASP cc_start: 0.8965 (t70) cc_final: 0.8569 (t0) REVERT: K 4 MET cc_start: 0.7391 (ptp) cc_final: 0.7147 (ptp) REVERT: K 72 THR cc_start: 0.8508 (m) cc_final: 0.8177 (p) REVERT: K 104 VAL cc_start: 0.7882 (p) cc_final: 0.7589 (t) REVERT: I 51 ILE cc_start: 0.8607 (tt) cc_final: 0.8337 (tt) REVERT: I 58 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7481 (ttm170) outliers start: 65 outliers final: 54 residues processed: 324 average time/residue: 0.3285 time to fit residues: 166.8756 Evaluate side-chains 330 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 274 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 82 SER Chi-restraints excluded: chain I residue 103 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 141 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 136 optimal weight: 10.0000 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 155 optimal weight: 10.0000 chunk 112 optimal weight: 0.4980 chunk 21 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 207 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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** C 105 HIS ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20622 Z= 0.238 Angle : 0.605 13.046 28011 Z= 0.310 Chirality : 0.044 0.197 3441 Planarity : 0.004 0.039 3429 Dihedral : 5.754 51.165 4665 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.43 % Favored : 95.14 % Rotamer: Outliers : 3.60 % Allowed : 14.18 % Favored : 82.22 % 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 (0.18), residues: 2346 helix: 0.72 (0.28), residues: 396 sheet: 0.32 (0.18), residues: 795 loop : -0.34 (0.20), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 103 HIS 0.002 0.001 HIS C 330 PHE 0.015 0.002 PHE G 100C TYR 0.015 0.001 TYR I 50 ARG 0.003 0.000 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 287 time to evaluate : 2.265 Fit side-chains REVERT: A 150 MET cc_start: 0.7938 (mmm) cc_final: 0.7368 (mmt) REVERT: B 652 GLN cc_start: 0.8730 (tp40) cc_final: 0.8381 (tp40) REVERT: B 659 ASP cc_start: 0.9025 (t70) cc_final: 0.8579 (t0) REVERT: C 95 MET cc_start: 0.8638 (ptm) cc_final: 0.8133 (ttm) REVERT: C 150 MET cc_start: 0.7960 (mmm) cc_final: 0.7635 (mmt) REVERT: C 426 MET cc_start: 0.5623 (tpp) cc_final: 0.5361 (mmt) REVERT: E 655 LYS cc_start: 0.8749 (mtpp) cc_final: 0.8455 (ttmt) REVERT: E 659 ASP cc_start: 0.8923 (t70) cc_final: 0.8389 (t0) REVERT: J 3 ARG cc_start: 0.6462 (mmp-170) cc_final: 0.6210 (mmp-170) REVERT: J 61 ARG cc_start: 0.7727 (mtp180) cc_final: 0.7419 (mtm110) REVERT: G 51 ILE cc_start: 0.8688 (tt) cc_final: 0.8428 (tt) REVERT: G 58 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7701 (ttm170) REVERT: D 150 MET cc_start: 0.8093 (mmm) cc_final: 0.7559 (mmt) REVERT: F 652 GLN cc_start: 0.8751 (tp40) cc_final: 0.8505 (tp40) REVERT: F 659 ASP cc_start: 0.9022 (t70) cc_final: 0.8654 (t0) REVERT: K 72 THR cc_start: 0.8508 (m) cc_final: 0.8186 (p) REVERT: K 104 VAL cc_start: 0.7843 (p) cc_final: 0.7552 (t) REVERT: I 58 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7539 (ttm170) outliers start: 76 outliers final: 64 residues processed: 330 average time/residue: 0.3058 time to fit residues: 156.7271 Evaluate side-chains 341 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 275 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 103 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 218 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 212 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 92 optimal weight: 0.3980 chunk 167 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 192 optimal weight: 2.9990 chunk 201 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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** H 77 GLN D 105 HIS ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 20622 Z= 0.236 Angle : 0.613 17.495 28011 Z= 0.313 Chirality : 0.044 0.186 3441 Planarity : 0.004 0.039 3429 Dihedral : 5.672 40.205 4665 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.35 % Favored : 95.23 % Rotamer: Outliers : 3.70 % Allowed : 14.51 % Favored : 81.79 % 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: -0.07 (0.18), residues: 2346 helix: 0.75 (0.28), residues: 396 sheet: 0.24 (0.17), residues: 801 loop : -0.46 (0.20), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 103 HIS 0.003 0.001 HIS D 249 PHE 0.016 0.001 PHE D 210 TYR 0.014 0.001 TYR H 91 ARG 0.002 0.000 ARG G 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 276 time to evaluate : 2.192 Fit side-chains REVERT: A 150 MET cc_start: 0.7937 (mmm) cc_final: 0.7363 (mmt) REVERT: B 652 GLN cc_start: 0.8708 (tp40) cc_final: 0.8389 (tp40) REVERT: B 659 ASP cc_start: 0.8989 (t70) cc_final: 0.8524 (t0) REVERT: C 95 MET cc_start: 0.8631 (ptm) cc_final: 0.8109 (ttm) REVERT: C 150 MET cc_start: 0.7969 (mmm) cc_final: 0.7650 (mmt) REVERT: E 655 LYS cc_start: 0.8776 (mtpp) cc_final: 0.8493 (ttmt) REVERT: E 659 ASP cc_start: 0.8919 (t70) cc_final: 0.8392 (t0) REVERT: J 61 ARG cc_start: 0.7735 (mtp180) cc_final: 0.7427 (mtm110) REVERT: G 51 ILE cc_start: 0.8676 (tt) cc_final: 0.8416 (tt) REVERT: G 58 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7687 (ttm170) REVERT: D 150 MET cc_start: 0.8126 (mmm) cc_final: 0.7601 (mmt) REVERT: F 652 GLN cc_start: 0.8752 (tp40) cc_final: 0.8513 (tp40) REVERT: F 659 ASP cc_start: 0.9020 (t70) cc_final: 0.8651 (t0) REVERT: K 72 THR cc_start: 0.8500 (m) cc_final: 0.8153 (p) REVERT: K 100 GLN cc_start: 0.7881 (pm20) cc_final: 0.6249 (mp10) REVERT: K 104 VAL cc_start: 0.7823 (p) cc_final: 0.7524 (t) REVERT: I 58 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7151 (ttm-80) outliers start: 78 outliers final: 71 residues processed: 323 average time/residue: 0.2977 time to fit residues: 149.4940 Evaluate side-chains 342 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 269 time to evaluate : 2.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 626 MET Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 569 THR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain G residue 15 SER Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain I residue 12 VAL Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 58 ARG Chi-restraints excluded: chain I residue 103 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 137 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 156 optimal weight: 0.7980 chunk 236 optimal weight: 0.9980 chunk 217 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 145 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 chunk 200 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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** C 103 GLN E 543 ASN ** F 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.4977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20622 Z= 0.167 Angle : 0.580 16.355 28011 Z= 0.297 Chirality : 0.043 0.179 3441 Planarity : 0.003 0.040 3429 Dihedral : 5.350 39.647 4665 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.43 % Allowed : 3.84 % Favored : 95.74 % Rotamer: Outliers : 3.08 % Allowed : 15.32 % Favored : 81.60 % 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: 0.10 (0.18), residues: 2346 helix: 0.92 (0.28), residues: 399 sheet: 0.40 (0.18), residues: 825 loop : -0.42 (0.20), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.003 0.001 HIS C 105 PHE 0.014 0.001 PHE D 210 TYR 0.017 0.001 TYR G 50 ARG 0.006 0.000 ARG H 58 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4692 Ramachandran restraints generated. 2346 Oldfield, 0 Emsley, 2346 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 288 time to evaluate : 2.166 Fit side-chains revert: symmetry clash REVERT: A 150 MET cc_start: 0.7906 (mmm) cc_final: 0.7376 (mmt) REVERT: B 652 GLN cc_start: 0.8670 (tp40) cc_final: 0.8394 (tp40) REVERT: B 659 ASP cc_start: 0.8936 (t70) cc_final: 0.8526 (t0) REVERT: C 95 MET cc_start: 0.8596 (ptm) cc_final: 0.8097 (ttm) REVERT: C 150 MET cc_start: 0.7941 (mmm) cc_final: 0.7531 (mmt) REVERT: C 426 MET cc_start: 0.5745 (mmt) cc_final: 0.5488 (mmt) REVERT: C 484 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7054 (t80) REVERT: E 655 LYS cc_start: 0.8735 (mtpp) cc_final: 0.8443 (ttmt) REVERT: E 659 ASP cc_start: 0.8875 (t70) cc_final: 0.8438 (t0) REVERT: J 61 ARG cc_start: 0.7765 (mtp180) cc_final: 0.7473 (mtm110) REVERT: G 51 ILE cc_start: 0.8598 (tt) cc_final: 0.8354 (tt) REVERT: G 58 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7894 (ttm170) REVERT: D 150 MET cc_start: 0.8097 (mmm) cc_final: 0.7663 (mmt) REVERT: D 217 TYR cc_start: 0.9157 (m-80) cc_final: 0.8471 (m-80) REVERT: F 652 GLN cc_start: 0.8701 (tp40) cc_final: 0.8368 (tp40) REVERT: F 659 ASP cc_start: 0.9000 (t70) cc_final: 0.8633 (t0) REVERT: K 72 THR cc_start: 0.8408 (m) cc_final: 0.8084 (p) REVERT: K 104 VAL cc_start: 0.7771 (p) cc_final: 0.7490 (t) outliers start: 65 outliers final: 61 residues processed: 325 average time/residue: 0.3120 time to fit residues: 157.9923 Evaluate side-chains 340 residues out of total 2109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 277 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 141 ASP Chi-restraints excluded: chain A residue 180 ASP Chi-restraints excluded: chain A residue 182 VAL Chi-restraints excluded: chain A residue 239 CYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 368 ASP Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 484 TYR Chi-restraints excluded: chain B residue 605 CYS Chi-restraints excluded: chain B residue 606 THR Chi-restraints excluded: chain B residue 625 ASN Chi-restraints excluded: chain B residue 635 ILE Chi-restraints excluded: chain L residue 6 GLN Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 91 GLU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 73 THR Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 141 ASP Chi-restraints excluded: chain C residue 180 ASP Chi-restraints excluded: chain C residue 182 VAL Chi-restraints excluded: chain C residue 239 CYS Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 346 VAL Chi-restraints excluded: chain C residue 373 THR Chi-restraints excluded: chain C residue 484 TYR Chi-restraints excluded: chain E residue 605 CYS Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain J residue 6 GLN Chi-restraints excluded: chain J residue 53 SER Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain G residue 21 THR Chi-restraints excluded: chain G residue 58 ARG Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 81 LYS Chi-restraints excluded: chain G residue 82 SER Chi-restraints excluded: chain G residue 103 TRP Chi-restraints excluded: chain D residue 141 ASP Chi-restraints excluded: chain D residue 180 ASP Chi-restraints excluded: chain D residue 182 VAL Chi-restraints excluded: chain D residue 213 ILE Chi-restraints excluded: chain D residue 239 CYS Chi-restraints excluded: chain D residue 294 ILE Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 373 THR Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 484 TYR Chi-restraints excluded: chain F residue 569 THR Chi-restraints excluded: chain F residue 605 CYS Chi-restraints excluded: chain F residue 625 ASN Chi-restraints excluded: chain F residue 635 ILE Chi-restraints excluded: chain K residue 6 GLN Chi-restraints excluded: chain K residue 53 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 75 ILE Chi-restraints excluded: chain I residue 103 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 57 optimal weight: 9.9990 chunk 173 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 0.0870 chunk 188 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 193 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 165 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 overall best weight: 2.4164 ------------------------------------------------------------------------------- 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** A 478 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.129016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.103766 restraints weight = 31206.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.105154 restraints weight = 23269.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.106895 restraints weight = 18175.655| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 20622 Z= 0.314 Angle : 0.653 15.657 28011 Z= 0.333 Chirality : 0.045 0.196 3441 Planarity : 0.004 0.039 3429 Dihedral : 5.722 42.932 4665 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.43 % Allowed : 4.90 % Favored : 94.67 % Rotamer: Outliers : 3.32 % Allowed : 15.50 % Favored : 81.18 % 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 (0.18), residues: 2346 helix: 0.64 (0.28), residues: 399 sheet: 0.26 (0.18), residues: 795 loop : -0.51 (0.20), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 103 HIS 0.003 0.001 HIS D 105 PHE 0.021 0.002 PHE D 53 TYR 0.015 0.002 TYR H 91 ARG 0.002 0.000 ARG H 100B Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3935.03 seconds wall clock time: 72 minutes 50.84 seconds (4370.84 seconds total)