Starting phenix.real_space_refine on Sat Mar 16 00:01:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca9_16521/03_2024/8ca9_16521_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca9_16521/03_2024/8ca9_16521.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca9_16521/03_2024/8ca9_16521.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca9_16521/03_2024/8ca9_16521.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca9_16521/03_2024/8ca9_16521_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ca9_16521/03_2024/8ca9_16521_trim.pdb" } resolution = 2.29 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= 0.008 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: 6 Type Number sf(0) Gaussians Cu 3 5.60 5 S 33 5.16 5 C 23217 2.51 5 N 5505 2.21 5 O 8827 1.98 5 H 33094 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 632": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 693": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 18": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 407": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 510": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 575": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 691": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 70679 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 11328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 11328 Classifications: {'peptide': 680} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 642} Chain: "B" Number of atoms: 11328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 11328 Classifications: {'peptide': 680} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 642} Chain: "C" Number of atoms: 11329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 11329 Classifications: {'peptide': 680} Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 642} Chain: "D" Number of atoms: 11262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 11262 Classifications: {'peptide': 678} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 643} Chain: "E" Number of atoms: 11262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 11262 Classifications: {'peptide': 678} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 643} Chain: "F" Number of atoms: 11262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 678, 11262 Classifications: {'peptide': 678} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 643} Chain: "G" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "H" 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: "I" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "J" 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: "K" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 83 Unusual residues: {'BMA': 1, 'MAN': 4, 'NAG': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "L" 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: "M" 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: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 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: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 364 Classifications: {'water': 364} Link IDs: {None: 363} Chain: "B" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 376 Classifications: {'water': 376} Link IDs: {None: 375} Chain: "C" Number of atoms: 348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 348 Classifications: {'water': 348} Link IDs: {None: 347} Chain: "D" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 337 Classifications: {'water': 337} Link IDs: {None: 336} Chain: "E" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 343 Classifications: {'water': 343} Link IDs: {None: 342} Chain: "F" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 339 Classifications: {'water': 339} Link IDs: {None: 338} Time building chain proxies: 22.84, per 1000 atoms: 0.32 Number of scatterers: 70679 At special positions: 0 Unit cell: (139.527, 141.159, 119.945, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 3 28.99 S 33 16.00 O 8827 8.00 N 5505 7.00 C 23217 6.00 H 33094 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 G 4 " - " MAN G 5 " " MAN I 4 " - " MAN I 5 " " MAN K 4 " - " MAN K 5 " " MAN M 4 " - " MAN M 5 " " MAN O 4 " - " MAN O 5 " " MAN Q 4 " - " MAN Q 5 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 6 " - " MAN G 7 " " BMA H 3 " - " MAN H 6 " " MAN H 4 " - " MAN H 5 " " BMA I 3 " - " MAN I 4 " " MAN I 6 " - " MAN I 7 " " BMA J 3 " - " MAN J 6 " " MAN J 4 " - " MAN J 5 " " BMA K 3 " - " MAN K 4 " " MAN K 6 " - " MAN K 7 " " BMA L 3 " - " MAN L 6 " " MAN L 4 " - " MAN L 5 " " BMA M 3 " - " MAN M 4 " " BMA O 3 " - " MAN O 4 " " BMA Q 3 " - " MAN Q 4 " ALPHA1-6 " BMA G 3 " - " MAN G 6 " " BMA H 3 " - " MAN H 4 " " BMA I 3 " - " MAN I 6 " " BMA J 3 " - " MAN J 4 " " BMA K 3 " - " MAN K 6 " " BMA L 3 " - " MAN L 4 " " BMA M 3 " - " MAN M 6 " " BMA O 3 " - " MAN O 6 " " BMA Q 3 " - " MAN Q 6 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG G 1 " - " ASN A 211 " " NAG H 1 " - " ASN A 481 " " NAG I 1 " - " ASN B 211 " " NAG J 1 " - " ASN B 481 " " NAG K 1 " - " ASN C 211 " " NAG L 1 " - " ASN C 481 " " NAG M 1 " - " ASN D 211 " " NAG N 1 " - " ASN D 479 " " NAG O 1 " - " ASN E 211 " " NAG P 1 " - " ASN E 479 " " NAG Q 1 " - " ASN F 211 " " NAG R 1 " - " ASN F 479 " Time building additional restraints: 43.47 Conformation dependent library (CDL) restraints added in 5.7 seconds 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7794 Finding SS restraints... Secondary structure from input PDB file: 219 helices and 39 sheets defined 49.0% alpha, 14.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.69 Creating SS restraints... Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 34 through 45 removed outlier: 3.889A pdb=" N THR A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 64 removed outlier: 3.768A pdb=" N LYS A 59 " --> pdb=" O ASP A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 73 removed outlier: 5.162A pdb=" N GLU A 71 " --> pdb=" O ALA A 68 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR A 73 " --> pdb=" O MET A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 89 removed outlier: 4.156A pdb=" N VAL A 79 " --> pdb=" O ASN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 117 Processing helix chain 'A' and resid 120 through 135 Processing helix chain 'A' and resid 136 through 151 Processing helix chain 'A' and resid 161 through 166 Processing helix chain 'A' and resid 167 through 171 removed outlier: 4.106A pdb=" N MET A 171 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 186 Processing helix chain 'A' and resid 190 through 197 Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 221 through 224 Processing helix chain 'A' and resid 225 through 230 Processing helix chain 'A' and resid 231 through 245 Processing helix chain 'A' and resid 250 through 255 Processing helix chain 'A' and resid 258 through 260 No H-bonds generated for 'chain 'A' and resid 258 through 260' Processing helix chain 'A' and resid 261 through 284 removed outlier: 3.715A pdb=" N TYR A 270 " --> pdb=" O TYR A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 348 removed outlier: 4.591A pdb=" N ASN A 329 " --> pdb=" O GLY A 325 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASP A 330 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 363 No H-bonds generated for 'chain 'A' and resid 361 through 363' Processing helix chain 'A' and resid 364 through 374 Processing helix chain 'A' and resid 375 through 380 removed outlier: 3.584A pdb=" N GLU A 380 " --> pdb=" O ASP A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 401 removed outlier: 3.889A pdb=" N ALA A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 409 removed outlier: 3.584A pdb=" N ILE A 407 " --> pdb=" O PRO A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 420 removed outlier: 3.756A pdb=" N PHE A 420 " --> pdb=" O ALA A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 426 Processing helix chain 'A' and resid 427 through 446 removed outlier: 4.284A pdb=" N TYR A 431 " --> pdb=" O ASP A 427 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN A 432 " --> pdb=" O PRO A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 483 through 486 Processing helix chain 'A' and resid 489 through 496 Processing helix chain 'A' and resid 544 through 549 Processing helix chain 'A' and resid 550 through 552 No H-bonds generated for 'chain 'A' and resid 550 through 552' Processing helix chain 'A' and resid 574 through 576 No H-bonds generated for 'chain 'A' and resid 574 through 576' Processing helix chain 'A' and resid 585 through 595 Processing helix chain 'A' and resid 600 through 605 Processing helix chain 'A' and resid 612 through 614 No H-bonds generated for 'chain 'A' and resid 612 through 614' Processing helix chain 'A' and resid 664 through 669 removed outlier: 3.613A pdb=" N ASN A 669 " --> pdb=" O TYR A 666 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 34 through 45 removed outlier: 3.889A pdb=" N THR B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 64 removed outlier: 3.767A pdb=" N LYS B 59 " --> pdb=" O ASP B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 73 removed outlier: 5.163A pdb=" N GLU B 71 " --> pdb=" O ALA B 68 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR B 73 " --> pdb=" O MET B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 89 removed outlier: 4.157A pdb=" N VAL B 79 " --> pdb=" O ASN B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 117 Processing helix chain 'B' and resid 120 through 135 Processing helix chain 'B' and resid 136 through 151 Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'B' and resid 167 through 171 removed outlier: 4.106A pdb=" N MET B 171 " --> pdb=" O GLU B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 186 Processing helix chain 'B' and resid 190 through 197 Proline residue: B 195 - end of helix Processing helix chain 'B' and resid 221 through 224 Processing helix chain 'B' and resid 225 through 230 Processing helix chain 'B' and resid 231 through 245 Processing helix chain 'B' and resid 250 through 255 Processing helix chain 'B' and resid 258 through 260 No H-bonds generated for 'chain 'B' and resid 258 through 260' Processing helix chain 'B' and resid 261 through 284 removed outlier: 3.717A pdb=" N TYR B 270 " --> pdb=" O TYR B 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 348 removed outlier: 4.590A pdb=" N ASN B 329 " --> pdb=" O GLY B 325 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASP B 330 " --> pdb=" O ASP B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 363 No H-bonds generated for 'chain 'B' and resid 361 through 363' Processing helix chain 'B' and resid 364 through 374 Processing helix chain 'B' and resid 375 through 380 removed outlier: 3.584A pdb=" N GLU B 380 " --> pdb=" O ASP B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 401 removed outlier: 3.890A pdb=" N ALA B 401 " --> pdb=" O ARG B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 409 removed outlier: 3.585A pdb=" N ILE B 407 " --> pdb=" O PRO B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 420 removed outlier: 3.756A pdb=" N PHE B 420 " --> pdb=" O ALA B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 426 Processing helix chain 'B' and resid 427 through 446 removed outlier: 4.283A pdb=" N TYR B 431 " --> pdb=" O ASP B 427 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN B 432 " --> pdb=" O PRO B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 457 Processing helix chain 'B' and resid 483 through 486 Processing helix chain 'B' and resid 489 through 496 Processing helix chain 'B' and resid 544 through 549 Processing helix chain 'B' and resid 550 through 552 No H-bonds generated for 'chain 'B' and resid 550 through 552' Processing helix chain 'B' and resid 574 through 576 No H-bonds generated for 'chain 'B' and resid 574 through 576' Processing helix chain 'B' and resid 585 through 595 Processing helix chain 'B' and resid 600 through 605 Processing helix chain 'B' and resid 612 through 614 No H-bonds generated for 'chain 'B' and resid 612 through 614' Processing helix chain 'B' and resid 664 through 669 removed outlier: 3.611A pdb=" N ASN B 669 " --> pdb=" O TYR B 666 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 34 through 45 removed outlier: 3.889A pdb=" N THR C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 64 removed outlier: 3.768A pdb=" N LYS C 59 " --> pdb=" O ASP C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 73 removed outlier: 5.163A pdb=" N GLU C 71 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 73 " --> pdb=" O MET C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 89 removed outlier: 4.156A pdb=" N VAL C 79 " --> pdb=" O ASN C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 101 through 117 Processing helix chain 'C' and resid 120 through 135 Processing helix chain 'C' and resid 136 through 151 Processing helix chain 'C' and resid 161 through 166 Processing helix chain 'C' and resid 167 through 171 removed outlier: 4.107A pdb=" N MET C 171 " --> pdb=" O GLU C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 186 Processing helix chain 'C' and resid 190 through 197 Proline residue: C 195 - end of helix Processing helix chain 'C' and resid 221 through 224 Processing helix chain 'C' and resid 225 through 230 Processing helix chain 'C' and resid 231 through 245 Processing helix chain 'C' and resid 250 through 255 Processing helix chain 'C' and resid 258 through 260 No H-bonds generated for 'chain 'C' and resid 258 through 260' Processing helix chain 'C' and resid 261 through 284 removed outlier: 3.716A pdb=" N TYR C 270 " --> pdb=" O TYR C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 348 removed outlier: 4.591A pdb=" N ASN C 329 " --> pdb=" O GLY C 325 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ASP C 330 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 363 No H-bonds generated for 'chain 'C' and resid 361 through 363' Processing helix chain 'C' and resid 364 through 374 Processing helix chain 'C' and resid 375 through 380 removed outlier: 3.585A pdb=" N GLU C 380 " --> pdb=" O ASP C 377 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 401 removed outlier: 3.889A pdb=" N ALA C 401 " --> pdb=" O ARG C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 409 removed outlier: 3.585A pdb=" N ILE C 407 " --> pdb=" O PRO C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 420 removed outlier: 3.756A pdb=" N PHE C 420 " --> pdb=" O ALA C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 423 through 426 Processing helix chain 'C' and resid 427 through 446 removed outlier: 4.283A pdb=" N TYR C 431 " --> pdb=" O ASP C 427 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN C 432 " --> pdb=" O PRO C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 457 Processing helix chain 'C' and resid 483 through 486 Processing helix chain 'C' and resid 489 through 496 Processing helix chain 'C' and resid 544 through 549 Processing helix chain 'C' and resid 550 through 552 No H-bonds generated for 'chain 'C' and resid 550 through 552' Processing helix chain 'C' and resid 574 through 576 No H-bonds generated for 'chain 'C' and resid 574 through 576' Processing helix chain 'C' and resid 585 through 595 Processing helix chain 'C' and resid 600 through 605 Processing helix chain 'C' and resid 612 through 614 No H-bonds generated for 'chain 'C' and resid 612 through 614' Processing helix chain 'C' and resid 664 through 669 removed outlier: 3.612A pdb=" N ASN C 669 " --> pdb=" O TYR C 666 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 55 through 64 removed outlier: 4.337A pdb=" N LYS D 59 " --> pdb=" O ASP D 55 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 73 removed outlier: 5.010A pdb=" N GLU D 71 " --> pdb=" O ALA D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 89 removed outlier: 4.151A pdb=" N VAL D 79 " --> pdb=" O ASN D 75 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR D 88 " --> pdb=" O SER D 84 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 117 Processing helix chain 'D' and resid 120 through 135 Processing helix chain 'D' and resid 136 through 151 Processing helix chain 'D' and resid 161 through 166 Processing helix chain 'D' and resid 167 through 170 Processing helix chain 'D' and resid 172 through 186 removed outlier: 3.504A pdb=" N LEU D 176 " --> pdb=" O ASN D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 195 removed outlier: 3.772A pdb=" N ALA D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN D 195 " --> pdb=" O PRO D 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 190 through 195' Processing helix chain 'D' and resid 221 through 224 Processing helix chain 'D' and resid 225 through 230 Processing helix chain 'D' and resid 231 through 245 removed outlier: 3.700A pdb=" N TYR D 238 " --> pdb=" O TRP D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 255 Processing helix chain 'D' and resid 261 through 284 Processing helix chain 'D' and resid 327 through 348 removed outlier: 3.695A pdb=" N PHE D 341 " --> pdb=" O TYR D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 363 No H-bonds generated for 'chain 'D' and resid 361 through 363' Processing helix chain 'D' and resid 364 through 374 Processing helix chain 'D' and resid 375 through 380 Processing helix chain 'D' and resid 390 through 401 removed outlier: 3.916A pdb=" N ALA D 401 " --> pdb=" O ARG D 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 418 Processing helix chain 'D' and resid 421 through 424 Processing helix chain 'D' and resid 425 through 444 removed outlier: 3.927A pdb=" N TYR D 429 " --> pdb=" O ASP D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 455 Processing helix chain 'D' and resid 481 through 484 Processing helix chain 'D' and resid 487 through 493 Processing helix chain 'D' and resid 542 through 547 Processing helix chain 'D' and resid 572 through 574 No H-bonds generated for 'chain 'D' and resid 572 through 574' Processing helix chain 'D' and resid 583 through 592 Processing helix chain 'D' and resid 598 through 602 Processing helix chain 'D' and resid 610 through 612 No H-bonds generated for 'chain 'D' and resid 610 through 612' Processing helix chain 'D' and resid 639 through 643 Processing helix chain 'D' and resid 662 through 667 Processing helix chain 'D' and resid 690 through 694 removed outlier: 3.579A pdb=" N GLN D 694 " --> pdb=" O TYR D 691 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 34 through 46 Processing helix chain 'E' and resid 55 through 64 removed outlier: 4.338A pdb=" N LYS E 59 " --> pdb=" O ASP E 55 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 73 removed outlier: 5.010A pdb=" N GLU E 71 " --> pdb=" O ALA E 68 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 89 removed outlier: 4.151A pdb=" N VAL E 79 " --> pdb=" O ASN E 75 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR E 88 " --> pdb=" O SER E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 117 Processing helix chain 'E' and resid 120 through 135 Processing helix chain 'E' and resid 136 through 151 Processing helix chain 'E' and resid 161 through 166 Processing helix chain 'E' and resid 167 through 170 Processing helix chain 'E' and resid 172 through 186 removed outlier: 3.504A pdb=" N LEU E 176 " --> pdb=" O ASN E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 195 removed outlier: 3.772A pdb=" N ALA E 194 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLN E 195 " --> pdb=" O PRO E 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 190 through 195' Processing helix chain 'E' and resid 221 through 224 Processing helix chain 'E' and resid 225 through 230 Processing helix chain 'E' and resid 231 through 245 removed outlier: 3.700A pdb=" N TYR E 238 " --> pdb=" O TRP E 234 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 255 Processing helix chain 'E' and resid 261 through 284 Processing helix chain 'E' and resid 327 through 348 removed outlier: 3.694A pdb=" N PHE E 341 " --> pdb=" O TYR E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 363 No H-bonds generated for 'chain 'E' and resid 361 through 363' Processing helix chain 'E' and resid 364 through 374 Processing helix chain 'E' and resid 375 through 380 Processing helix chain 'E' and resid 390 through 401 removed outlier: 3.916A pdb=" N ALA E 401 " --> pdb=" O ARG E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 414 through 418 Processing helix chain 'E' and resid 421 through 424 Processing helix chain 'E' and resid 425 through 444 removed outlier: 3.926A pdb=" N TYR E 429 " --> pdb=" O ASP E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 450 through 455 Processing helix chain 'E' and resid 481 through 484 Processing helix chain 'E' and resid 487 through 493 Processing helix chain 'E' and resid 542 through 547 Processing helix chain 'E' and resid 572 through 574 No H-bonds generated for 'chain 'E' and resid 572 through 574' Processing helix chain 'E' and resid 583 through 592 Processing helix chain 'E' and resid 598 through 602 Processing helix chain 'E' and resid 610 through 612 No H-bonds generated for 'chain 'E' and resid 610 through 612' Processing helix chain 'E' and resid 639 through 643 Processing helix chain 'E' and resid 662 through 667 Processing helix chain 'E' and resid 690 through 694 removed outlier: 3.579A pdb=" N GLN E 694 " --> pdb=" O TYR E 691 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 34 through 46 Processing helix chain 'F' and resid 55 through 64 removed outlier: 4.337A pdb=" N LYS F 59 " --> pdb=" O ASP F 55 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ILE F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 66 through 73 removed outlier: 5.011A pdb=" N GLU F 71 " --> pdb=" O ALA F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 89 removed outlier: 4.151A pdb=" N VAL F 79 " --> pdb=" O ASN F 75 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR F 88 " --> pdb=" O SER F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 117 Processing helix chain 'F' and resid 120 through 135 Processing helix chain 'F' and resid 136 through 151 Processing helix chain 'F' and resid 161 through 166 Processing helix chain 'F' and resid 167 through 170 Processing helix chain 'F' and resid 172 through 186 removed outlier: 3.505A pdb=" N LEU F 176 " --> pdb=" O ASN F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 195 removed outlier: 3.773A pdb=" N ALA F 194 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN F 195 " --> pdb=" O PRO F 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 190 through 195' Processing helix chain 'F' and resid 221 through 224 Processing helix chain 'F' and resid 225 through 230 Processing helix chain 'F' and resid 231 through 245 removed outlier: 3.700A pdb=" N TYR F 238 " --> pdb=" O TRP F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 255 Processing helix chain 'F' and resid 261 through 284 Processing helix chain 'F' and resid 327 through 348 removed outlier: 3.695A pdb=" N PHE F 341 " --> pdb=" O TYR F 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 361 through 363 No H-bonds generated for 'chain 'F' and resid 361 through 363' Processing helix chain 'F' and resid 364 through 374 Processing helix chain 'F' and resid 375 through 380 Processing helix chain 'F' and resid 390 through 401 removed outlier: 3.916A pdb=" N ALA F 401 " --> pdb=" O ARG F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 418 Processing helix chain 'F' and resid 421 through 424 Processing helix chain 'F' and resid 425 through 444 removed outlier: 3.926A pdb=" N TYR F 429 " --> pdb=" O ASP F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 455 Processing helix chain 'F' and resid 481 through 484 Processing helix chain 'F' and resid 487 through 493 Processing helix chain 'F' and resid 542 through 547 Processing helix chain 'F' and resid 572 through 574 No H-bonds generated for 'chain 'F' and resid 572 through 574' Processing helix chain 'F' and resid 583 through 592 Processing helix chain 'F' and resid 598 through 602 Processing helix chain 'F' and resid 610 through 612 No H-bonds generated for 'chain 'F' and resid 610 through 612' Processing helix chain 'F' and resid 639 through 643 Processing helix chain 'F' and resid 662 through 667 Processing helix chain 'F' and resid 690 through 694 removed outlier: 3.579A pdb=" N GLN F 694 " --> pdb=" O TYR F 691 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 202 removed outlier: 6.260A pdb=" N TYR A 206 " --> pdb=" O ILE A 501 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ARG A 503 " --> pdb=" O TYR A 206 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N PHE A 208 " --> pdb=" O ARG A 503 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N LEU A 471 " --> pdb=" O TYR A 681 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N SER A 524 " --> pdb=" O LYS A 561 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LYS A 561 " --> pdb=" O SER A 524 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL A 526 " --> pdb=" O THR A 559 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR A 559 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 528 " --> pdb=" O TRP A 557 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TRP A 557 " --> pdb=" O VAL A 528 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE A 530 " --> pdb=" O LEU A 555 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 307 through 308 Processing sheet with id=AA4, first strand: chain 'A' and resid 349 through 352 Processing sheet with id=AA5, first strand: chain 'A' and resid 461 through 468 removed outlier: 5.583A pdb=" N ILE A 463 " --> pdb=" O LYS A 519 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS A 519 " --> pdb=" O ILE A 463 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP A 465 " --> pdb=" O ASP A 517 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 579 through 580 Processing sheet with id=AA7, first strand: chain 'B' and resid 27 through 29 Processing sheet with id=AA8, first strand: chain 'B' and resid 199 through 202 removed outlier: 6.261A pdb=" N TYR B 206 " --> pdb=" O ILE B 501 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG B 503 " --> pdb=" O TYR B 206 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N PHE B 208 " --> pdb=" O ARG B 503 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU B 471 " --> pdb=" O TYR B 681 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N SER B 524 " --> pdb=" O LYS B 561 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LYS B 561 " --> pdb=" O SER B 524 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 526 " --> pdb=" O THR B 559 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR B 559 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL B 528 " --> pdb=" O TRP B 557 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TRP B 557 " --> pdb=" O VAL B 528 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE B 530 " --> pdb=" O LEU B 555 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 307 through 308 Processing sheet with id=AB1, first strand: chain 'B' and resid 349 through 352 Processing sheet with id=AB2, first strand: chain 'B' and resid 461 through 468 removed outlier: 5.583A pdb=" N ILE B 463 " --> pdb=" O LYS B 519 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS B 519 " --> pdb=" O ILE B 463 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ASP B 465 " --> pdb=" O ASP B 517 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 579 through 580 Processing sheet with id=AB4, first strand: chain 'C' and resid 27 through 29 Processing sheet with id=AB5, first strand: chain 'C' and resid 199 through 202 removed outlier: 6.261A pdb=" N TYR C 206 " --> pdb=" O ILE C 501 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N ARG C 503 " --> pdb=" O TYR C 206 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N PHE C 208 " --> pdb=" O ARG C 503 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU C 471 " --> pdb=" O TYR C 681 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N SER C 524 " --> pdb=" O LYS C 561 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LYS C 561 " --> pdb=" O SER C 524 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL C 526 " --> pdb=" O THR C 559 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N THR C 559 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL C 528 " --> pdb=" O TRP C 557 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N TRP C 557 " --> pdb=" O VAL C 528 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE C 530 " --> pdb=" O LEU C 555 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 307 through 308 Processing sheet with id=AB7, first strand: chain 'C' and resid 349 through 352 Processing sheet with id=AB8, first strand: chain 'C' and resid 461 through 468 removed outlier: 5.584A pdb=" N ILE C 463 " --> pdb=" O LYS C 519 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LYS C 519 " --> pdb=" O ILE C 463 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP C 465 " --> pdb=" O ASP C 517 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 579 through 580 Processing sheet with id=AC1, first strand: chain 'D' and resid 27 through 29 Processing sheet with id=AC2, first strand: chain 'D' and resid 199 through 202 removed outlier: 6.190A pdb=" N TYR D 206 " --> pdb=" O ILE D 499 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ARG D 501 " --> pdb=" O TYR D 206 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N PHE D 208 " --> pdb=" O ARG D 501 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU D 469 " --> pdb=" O TYR D 679 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER D 522 " --> pdb=" O LYS D 559 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS D 559 " --> pdb=" O SER D 522 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA D 524 " --> pdb=" O THR D 557 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR D 557 " --> pdb=" O ALA D 524 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ILE D 526 " --> pdb=" O TRP D 555 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N TRP D 555 " --> pdb=" O ILE D 526 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE D 528 " --> pdb=" O ILE D 553 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 297 through 298 Processing sheet with id=AC4, first strand: chain 'D' and resid 307 through 308 Processing sheet with id=AC5, first strand: chain 'D' and resid 349 through 352 Processing sheet with id=AC6, first strand: chain 'D' and resid 460 through 466 removed outlier: 5.446A pdb=" N ILE D 461 " --> pdb=" O LYS D 517 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS D 517 " --> pdb=" O ILE D 461 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 577 through 578 Processing sheet with id=AC8, first strand: chain 'E' and resid 27 through 29 Processing sheet with id=AC9, first strand: chain 'E' and resid 199 through 202 removed outlier: 6.189A pdb=" N TYR E 206 " --> pdb=" O ILE E 499 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ARG E 501 " --> pdb=" O TYR E 206 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N PHE E 208 " --> pdb=" O ARG E 501 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU E 469 " --> pdb=" O TYR E 679 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N SER E 522 " --> pdb=" O LYS E 559 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS E 559 " --> pdb=" O SER E 522 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA E 524 " --> pdb=" O THR E 557 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR E 557 " --> pdb=" O ALA E 524 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE E 526 " --> pdb=" O TRP E 555 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TRP E 555 " --> pdb=" O ILE E 526 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE E 528 " --> pdb=" O ILE E 553 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 297 through 298 Processing sheet with id=AD2, first strand: chain 'E' and resid 307 through 308 Processing sheet with id=AD3, first strand: chain 'E' and resid 349 through 352 Processing sheet with id=AD4, first strand: chain 'E' and resid 460 through 466 removed outlier: 5.446A pdb=" N ILE E 461 " --> pdb=" O LYS E 517 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS E 517 " --> pdb=" O ILE E 461 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 577 through 578 Processing sheet with id=AD6, first strand: chain 'F' and resid 27 through 29 Processing sheet with id=AD7, first strand: chain 'F' and resid 199 through 202 removed outlier: 6.189A pdb=" N TYR F 206 " --> pdb=" O ILE F 499 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ARG F 501 " --> pdb=" O TYR F 206 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N PHE F 208 " --> pdb=" O ARG F 501 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N LEU F 469 " --> pdb=" O TYR F 679 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N SER F 522 " --> pdb=" O LYS F 559 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS F 559 " --> pdb=" O SER F 522 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA F 524 " --> pdb=" O THR F 557 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N THR F 557 " --> pdb=" O ALA F 524 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE F 526 " --> pdb=" O TRP F 555 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N TRP F 555 " --> pdb=" O ILE F 526 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ILE F 528 " --> pdb=" O ILE F 553 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 297 through 298 Processing sheet with id=AD9, first strand: chain 'F' and resid 307 through 308 Processing sheet with id=AE1, first strand: chain 'F' and resid 349 through 352 Processing sheet with id=AE2, first strand: chain 'F' and resid 460 through 466 removed outlier: 5.447A pdb=" N ILE F 461 " --> pdb=" O LYS F 517 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYS F 517 " --> pdb=" O ILE F 461 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 577 through 578 1422 hydrogen bonds defined for protein. 3888 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: 25.81 Time building geometry restraints manager: 45.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 33091 1.03 - 1.22: 1 1.22 - 1.42: 16612 1.42 - 1.61: 19914 1.61 - 1.81: 67 Bond restraints: 69685 Sorted by residual: bond pdb=" CD2 HIS B 242 " pdb=" HD2 HIS B 242 " ideal model delta sigma weight residual 0.930 1.660 -0.730 2.00e-02 2.50e+03 1.33e+03 bond pdb=" NE2 HIS B 242 " pdb=" HE2 HIS B 242 " ideal model delta sigma weight residual 0.860 1.344 -0.484 2.00e-02 2.50e+03 5.86e+02 bond pdb=" CE1 HIS B 242 " pdb=" HE1 HIS B 242 " ideal model delta sigma weight residual 0.930 1.156 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" ND1 HIS A 242 " pdb=" HD1 HIS A 242 " ideal model delta sigma weight residual 0.860 1.005 -0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" ND1 HIS C 242 " pdb=" HD1 HIS C 242 " ideal model delta sigma weight residual 0.860 1.004 -0.144 2.00e-02 2.50e+03 5.20e+01 ... (remaining 69680 not shown) Histogram of bond angle deviations from ideal: 16.63 - 48.30: 4 48.30 - 79.97: 8 79.97 - 111.65: 72760 111.65 - 143.32: 51950 143.32 - 174.99: 2 Bond angle restraints: 124724 Sorted by residual: angle pdb=" CG HIS B 242 " pdb=" CD2 HIS B 242 " pdb=" HD2 HIS B 242 " ideal model delta sigma weight residual 126.40 16.63 109.77 3.00e+00 1.11e-01 1.34e+03 angle pdb=" CG HIS A 242 " pdb=" ND1 HIS A 242 " pdb=" HD1 HIS A 242 " ideal model delta sigma weight residual 125.35 21.47 103.88 3.00e+00 1.11e-01 1.20e+03 angle pdb=" CG HIS C 242 " pdb=" ND1 HIS C 242 " pdb=" HD1 HIS C 242 " ideal model delta sigma weight residual 125.35 21.49 103.86 3.00e+00 1.11e-01 1.20e+03 angle pdb=" CE1 HIS B 242 " pdb=" NE2 HIS B 242 " pdb=" HE2 HIS B 242 " ideal model delta sigma weight residual 125.50 41.05 84.45 3.00e+00 1.11e-01 7.92e+02 angle pdb=" NE2 HIS A 242 " pdb=" CD2 HIS A 242 " pdb=" HD2 HIS A 242 " ideal model delta sigma weight residual 126.40 51.31 75.09 3.00e+00 1.11e-01 6.27e+02 ... (remaining 124719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.41: 33546 33.41 - 66.82: 593 66.82 - 100.24: 123 100.24 - 133.65: 60 133.65 - 167.06: 5 Dihedral angle restraints: 34327 sinusoidal: 18303 harmonic: 16024 Sorted by residual: dihedral pdb=" ND1 HIS C 242 " pdb=" CG HIS C 242 " pdb=" CD2 HIS C 242 " pdb=" HD2 HIS C 242 " ideal model delta harmonic sigma weight residual 180.00 12.94 167.06 0 5.00e+00 4.00e-02 1.12e+03 dihedral pdb=" ND1 HIS A 242 " pdb=" CG HIS A 242 " pdb=" CD2 HIS A 242 " pdb=" HD2 HIS A 242 " ideal model delta harmonic sigma weight residual 180.00 12.94 167.06 0 5.00e+00 4.00e-02 1.12e+03 dihedral pdb=" CG HIS B 242 " pdb=" ND1 HIS B 242 " pdb=" CE1 HIS B 242 " pdb=" HE1 HIS B 242 " ideal model delta harmonic sigma weight residual -180.00 -18.72 -161.28 0 5.00e+00 4.00e-02 1.04e+03 ... (remaining 34324 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 4525 0.058 - 0.116: 576 0.116 - 0.174: 116 0.174 - 0.232: 0 0.232 - 0.290: 12 Chirality restraints: 5229 Sorted by residual: chirality pdb=" C5 BMA O 3 " pdb=" C4 BMA O 3 " pdb=" C6 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.09e+00 chirality pdb=" C5 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C6 BMA Q 3 " pdb=" O5 BMA Q 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 5226 not shown) Planarity restraints: 10182 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 242 " 0.006 2.00e-02 2.50e+03 1.27e-01 3.62e+02 pdb=" CG HIS A 242 " 0.161 2.00e-02 2.50e+03 pdb=" ND1 HIS A 242 " 0.095 2.00e-02 2.50e+03 pdb=" CD2 HIS A 242 " -0.027 2.00e-02 2.50e+03 pdb=" CE1 HIS A 242 " 0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS A 242 " 0.163 2.00e-02 2.50e+03 pdb=" HD1 HIS A 242 " -0.128 2.00e-02 2.50e+03 pdb=" HD2 HIS A 242 " -0.254 2.00e-02 2.50e+03 pdb=" HE1 HIS A 242 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 242 " 0.006 2.00e-02 2.50e+03 1.27e-01 3.62e+02 pdb=" CG HIS B 242 " 0.162 2.00e-02 2.50e+03 pdb=" ND1 HIS B 242 " 0.095 2.00e-02 2.50e+03 pdb=" CD2 HIS B 242 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS B 242 " 0.019 2.00e-02 2.50e+03 pdb=" NE2 HIS B 242 " 0.162 2.00e-02 2.50e+03 pdb=" HD2 HIS B 242 " -0.128 2.00e-02 2.50e+03 pdb=" HE1 HIS B 242 " -0.254 2.00e-02 2.50e+03 pdb=" HE2 HIS B 242 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 242 " 0.006 2.00e-02 2.50e+03 1.27e-01 3.62e+02 pdb=" CG HIS C 242 " 0.161 2.00e-02 2.50e+03 pdb=" ND1 HIS C 242 " 0.095 2.00e-02 2.50e+03 pdb=" CD2 HIS C 242 " -0.026 2.00e-02 2.50e+03 pdb=" CE1 HIS C 242 " 0.020 2.00e-02 2.50e+03 pdb=" NE2 HIS C 242 " 0.162 2.00e-02 2.50e+03 pdb=" HD1 HIS C 242 " -0.128 2.00e-02 2.50e+03 pdb=" HD2 HIS C 242 " -0.254 2.00e-02 2.50e+03 pdb=" HE1 HIS C 242 " -0.037 2.00e-02 2.50e+03 ... (remaining 10179 not shown) Histogram of nonbonded interaction distances: 0.99 - 1.71: 64 1.71 - 2.43: 35447 2.43 - 3.16: 210092 3.16 - 3.88: 299937 3.88 - 4.60: 482976 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1028516 Sorted by model distance: nonbonded pdb=" CD2 HIS B 242 " pdb=" HE1 HIS B 242 " model vdw 0.991 2.240 nonbonded pdb=" ND1 HIS B 242 " pdb=" HD2 HIS B 242 " model vdw 1.005 2.080 nonbonded pdb=" CE1 HIS C 242 " pdb=" HD2 HIS C 242 " model vdw 1.156 2.240 nonbonded pdb=" CE1 HIS A 242 " pdb=" HD2 HIS A 242 " model vdw 1.156 2.240 nonbonded pdb=" CG HIS B 242 " pdb=" HE1 HIS B 242 " model vdw 1.313 2.240 ... (remaining 1028511 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and (resid 17 through 149 or (resid 150 and (name N or name CA or nam \ e C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name \ NE2 or name H or name HA or name HB2 or name HB3 or name HD2 or name HE1 or name \ HE2)) or resid 151 through 696 or resid 900)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 2 or resid 5 through 7)) selection = (chain 'H' and (resid 1 or resid 4 through 6)) selection = (chain 'I' and (resid 2 or resid 5 through 7)) selection = (chain 'J' and (resid 1 or resid 4 through 6)) selection = (chain 'K' and (resid 2 or resid 5 through 7)) selection = (chain 'L' and (resid 1 or resid 4 through 6)) selection = (chain 'M' and (resid 1 or resid 4 through 6)) selection = (chain 'O' and (resid 1 or resid 4 through 6)) selection = (chain 'Q' and (resid 1 or resid 4 through 6)) } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.820 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: 1.000 Extract box with map and model: 13.420 Check model and map are aligned: 0.810 Set scattering table: 0.510 Process input model: 170.830 Find NCS groups from input model: 2.740 Set up NCS constraints: 0.440 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: 0.020 Load rotamer database and sin/cos tables:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 203.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 : 0.003 0.061 36591 Z= 0.195 Angle : 0.563 6.865 49803 Z= 0.279 Chirality : 0.044 0.290 5229 Planarity : 0.004 0.072 6315 Dihedral : 14.411 110.112 14358 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 0.94 (0.13), residues: 4062 helix: 0.33 (0.14), residues: 1503 sheet: 1.06 (0.22), residues: 567 loop : 0.97 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 234 HIS 0.102 0.007 HIS A 242 PHE 0.010 0.001 PHE B 531 TYR 0.012 0.001 TYR D 266 ARG 0.002 0.000 ARG D 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 560 time to evaluate : 4.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 GLU cc_start: 0.7681 (mt-10) cc_final: 0.7461 (mt-10) REVERT: B 70 MET cc_start: 0.7084 (ttm) cc_final: 0.6749 (ttt) REVERT: B 95 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7386 (mt-10) REVERT: B 593 LEU cc_start: 0.8226 (tp) cc_final: 0.7957 (tm) REVERT: B 654 PHE cc_start: 0.8268 (m-80) cc_final: 0.8065 (m-80) REVERT: C 95 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7198 (mm-30) REVERT: C 593 LEU cc_start: 0.8238 (tp) cc_final: 0.7964 (tm) REVERT: C 602 MET cc_start: 0.8064 (mtp) cc_final: 0.7778 (mtp) REVERT: E 59 LYS cc_start: 0.7297 (tppt) cc_final: 0.7078 (tttm) REVERT: E 204 ASN cc_start: 0.6462 (t0) cc_final: 0.6152 (m110) REVERT: F 109 ARG cc_start: 0.7550 (ttm170) cc_final: 0.7205 (mtp-110) REVERT: F 190 LEU cc_start: 0.8025 (mt) cc_final: 0.7809 (mt) REVERT: F 204 ASN cc_start: 0.6316 (t0) cc_final: 0.5801 (t0) outliers start: 0 outliers final: 0 residues processed: 560 average time/residue: 2.9072 time to fit residues: 1942.6286 Evaluate side-chains 431 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 431 time to evaluate : 4.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 341 optimal weight: 4.9990 chunk 306 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 104 optimal weight: 0.3980 chunk 207 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 317 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 193 optimal weight: 0.9990 chunk 236 optimal weight: 6.9990 chunk 367 optimal weight: 6.9990 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 293 ASN A 413 ASN A 491 GLN A 595 ASN A 669 ASN B 491 GLN B 566 GLN B 595 ASN B 669 ASN C 204 ASN C 293 ASN C 566 GLN C 595 ASN C 696 GLN D 253 ASN D 346 GLN D 565 ASN D 593 ASN E 253 ASN E 489 GLN E 565 ASN E 593 ASN F 75 ASN F 253 ASN F 451 GLN F 565 ASN F 593 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36591 Z= 0.209 Angle : 0.584 11.495 49803 Z= 0.304 Chirality : 0.044 0.203 5229 Planarity : 0.004 0.042 6315 Dihedral : 10.859 78.460 6000 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.14 % Allowed : 7.44 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.13), residues: 4062 helix: 1.32 (0.13), residues: 1512 sheet: 0.92 (0.21), residues: 549 loop : 0.87 (0.14), residues: 2001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 234 HIS 0.024 0.002 HIS C 242 PHE 0.014 0.002 PHE A 97 TYR 0.021 0.002 TYR D 432 ARG 0.004 0.001 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 443 time to evaluate : 4.295 Fit side-chains revert: symmetry clash REVERT: A 70 MET cc_start: 0.7266 (ttm) cc_final: 0.7055 (ttt) REVERT: A 81 GLU cc_start: 0.7206 (OUTLIER) cc_final: 0.6856 (mt-10) REVERT: A 95 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7489 (mt-10) REVERT: B 70 MET cc_start: 0.7207 (ttm) cc_final: 0.6899 (ttt) REVERT: B 81 GLU cc_start: 0.7179 (OUTLIER) cc_final: 0.6743 (mt-10) REVERT: B 95 GLU cc_start: 0.7672 (mt-10) cc_final: 0.7398 (mt-10) REVERT: B 654 PHE cc_start: 0.8343 (m-80) cc_final: 0.8082 (m-80) REVERT: B 683 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.7289 (tm-30) REVERT: C 70 MET cc_start: 0.7191 (ttm) cc_final: 0.6911 (ttt) REVERT: C 77 GLU cc_start: 0.6689 (mp0) cc_final: 0.6278 (tt0) REVERT: C 81 GLU cc_start: 0.7239 (OUTLIER) cc_final: 0.6815 (mt-10) REVERT: C 95 GLU cc_start: 0.7643 (mt-10) cc_final: 0.7124 (mm-30) REVERT: C 439 ASP cc_start: 0.8078 (m-30) cc_final: 0.7860 (m-30) REVERT: C 593 LEU cc_start: 0.8228 (tp) cc_final: 0.7948 (tm) REVERT: C 683 GLU cc_start: 0.7548 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: D 109 ARG cc_start: 0.7533 (ttt180) cc_final: 0.7152 (mtp-110) REVERT: E 119 LYS cc_start: 0.7908 (ttmt) cc_final: 0.7707 (ttpt) REVERT: F 75 ASN cc_start: 0.6898 (OUTLIER) cc_final: 0.6480 (t0) REVERT: F 109 ARG cc_start: 0.7569 (ttm170) cc_final: 0.7156 (mtp-110) REVERT: F 204 ASN cc_start: 0.6448 (t0) cc_final: 0.6091 (t0) outliers start: 42 outliers final: 11 residues processed: 461 average time/residue: 2.8157 time to fit residues: 1560.8186 Evaluate side-chains 441 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 424 time to evaluate : 4.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 683 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 517 ASP Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain F residue 324 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 204 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 306 optimal weight: 5.9990 chunk 250 optimal weight: 6.9990 chunk 101 optimal weight: 5.9990 chunk 368 optimal weight: 4.9990 chunk 398 optimal weight: 3.9990 chunk 328 optimal weight: 10.0000 chunk 365 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 295 optimal weight: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 ASN A 635 GLN A 669 ASN B 669 ASN C 204 ASN C 566 GLN D 253 ASN D 593 ASN E 346 GLN E 489 GLN E 593 ASN F 451 GLN F 593 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.100 36591 Z= 0.251 Angle : 0.592 8.232 49803 Z= 0.320 Chirality : 0.044 0.175 5229 Planarity : 0.004 0.041 6315 Dihedral : 9.339 77.296 6000 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.35 % Allowed : 7.90 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.13), residues: 4062 helix: 1.15 (0.13), residues: 1527 sheet: 0.72 (0.21), residues: 552 loop : 0.75 (0.14), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 234 HIS 0.005 0.001 HIS C 242 PHE 0.019 0.002 PHE A 531 TYR 0.024 0.002 TYR D 432 ARG 0.006 0.001 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 446 time to evaluate : 4.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7349 (ttm) cc_final: 0.7116 (ttt) REVERT: A 81 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.6990 (mt-10) REVERT: A 523 GLU cc_start: 0.5695 (tt0) cc_final: 0.5474 (tt0) REVERT: A 597 GLN cc_start: 0.7312 (mt0) cc_final: 0.7009 (mt0) REVERT: B 70 MET cc_start: 0.7249 (ttm) cc_final: 0.6981 (ttt) REVERT: B 81 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6990 (mt-10) REVERT: B 95 GLU cc_start: 0.7666 (mt-10) cc_final: 0.7387 (mt-10) REVERT: B 525 GLU cc_start: 0.7069 (OUTLIER) cc_final: 0.6731 (mm-30) REVERT: B 651 ASN cc_start: 0.8551 (p0) cc_final: 0.8306 (p0) REVERT: B 654 PHE cc_start: 0.8391 (m-80) cc_final: 0.8086 (m-80) REVERT: B 683 GLU cc_start: 0.7537 (OUTLIER) cc_final: 0.7222 (tm-30) REVERT: C 70 MET cc_start: 0.7301 (ttm) cc_final: 0.7027 (ttt) REVERT: C 77 GLU cc_start: 0.6786 (mp0) cc_final: 0.6574 (tt0) REVERT: C 81 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.6993 (mt-10) REVERT: C 525 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6830 (mm-30) REVERT: C 593 LEU cc_start: 0.8253 (tp) cc_final: 0.7964 (tm) REVERT: C 654 PHE cc_start: 0.8321 (m-80) cc_final: 0.8116 (m-80) REVERT: C 683 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7324 (tm-30) REVERT: D 388 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7544 (mt) REVERT: D 675 ASP cc_start: 0.7630 (m-30) cc_final: 0.7394 (m-30) REVERT: E 388 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7408 (mt) REVERT: F 54 ASP cc_start: 0.7516 (m-30) cc_final: 0.7272 (m-30) REVERT: F 109 ARG cc_start: 0.7619 (ttm170) cc_final: 0.7250 (mtp-110) REVERT: F 204 ASN cc_start: 0.6703 (t0) cc_final: 0.6360 (t0) REVERT: F 618 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.6684 (mm-30) outliers start: 50 outliers final: 18 residues processed: 467 average time/residue: 2.8597 time to fit residues: 1601.4442 Evaluate side-chains 456 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 428 time to evaluate : 4.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 683 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 517 ASP Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 388 LEU Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain F residue 618 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 364 optimal weight: 5.9990 chunk 277 optimal weight: 6.9990 chunk 191 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 175 optimal weight: 0.4980 chunk 247 optimal weight: 0.9980 chunk 369 optimal weight: 6.9990 chunk 391 optimal weight: 6.9990 chunk 193 optimal weight: 4.9990 chunk 350 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 overall best weight: 3.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN A 669 ASN B 355 GLN B 669 ASN C 204 ASN C 355 GLN C 566 GLN C 669 ASN D 327 ASN D 593 ASN E 489 GLN E 593 ASN F 327 ASN F 593 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 36591 Z= 0.216 Angle : 0.559 6.378 49803 Z= 0.302 Chirality : 0.043 0.180 5229 Planarity : 0.004 0.039 6315 Dihedral : 8.753 76.508 6000 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.38 % Allowed : 8.09 % Favored : 90.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.13), residues: 4062 helix: 1.25 (0.13), residues: 1509 sheet: 0.62 (0.21), residues: 561 loop : 0.68 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 234 HIS 0.003 0.001 HIS C 242 PHE 0.015 0.002 PHE A 531 TYR 0.021 0.002 TYR D 432 ARG 0.007 0.001 ARG F 297 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 440 time to evaluate : 4.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7347 (ttm) cc_final: 0.7121 (ttt) REVERT: A 81 GLU cc_start: 0.7408 (OUTLIER) cc_final: 0.7030 (mt-10) REVERT: A 597 GLN cc_start: 0.7313 (mt0) cc_final: 0.7015 (mt0) REVERT: A 683 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7028 (tm-30) REVERT: B 70 MET cc_start: 0.7250 (ttm) cc_final: 0.6994 (ttt) REVERT: B 81 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.6965 (mt-10) REVERT: B 95 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7442 (mt-10) REVERT: B 467 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7926 (mtpp) REVERT: B 525 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.6702 (mm-30) REVERT: B 651 ASN cc_start: 0.8534 (p0) cc_final: 0.8312 (p0) REVERT: B 654 PHE cc_start: 0.8377 (m-80) cc_final: 0.8059 (m-80) REVERT: B 683 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7194 (tm-30) REVERT: C 70 MET cc_start: 0.7266 (ttm) cc_final: 0.7007 (ttt) REVERT: C 81 GLU cc_start: 0.7364 (OUTLIER) cc_final: 0.6952 (mt-10) REVERT: C 386 ASN cc_start: 0.8173 (m110) cc_final: 0.7927 (m-40) REVERT: C 525 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6783 (mm-30) REVERT: C 593 LEU cc_start: 0.8230 (tp) cc_final: 0.7956 (tm) REVERT: C 654 PHE cc_start: 0.8324 (m-80) cc_final: 0.8120 (m-80) REVERT: C 683 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7320 (tm-30) REVERT: D 675 ASP cc_start: 0.7726 (m-30) cc_final: 0.7486 (m-30) REVERT: E 95 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7509 (mt0) REVERT: E 388 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7403 (mt) REVERT: F 25 VAL cc_start: 0.7555 (OUTLIER) cc_final: 0.7142 (t) REVERT: F 54 ASP cc_start: 0.7522 (m-30) cc_final: 0.7293 (m-30) REVERT: F 109 ARG cc_start: 0.7628 (ttm170) cc_final: 0.7268 (mtp-110) REVERT: F 204 ASN cc_start: 0.6667 (t0) cc_final: 0.6377 (t0) outliers start: 51 outliers final: 19 residues processed: 467 average time/residue: 2.8634 time to fit residues: 1603.1471 Evaluate side-chains 456 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 425 time to evaluate : 4.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 467 LYS Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 683 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 260 GLU Chi-restraints excluded: chain C residue 525 GLU Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 220 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 326 optimal weight: 7.9990 chunk 222 optimal weight: 0.9990 chunk 5 optimal weight: 9.9990 chunk 291 optimal weight: 7.9990 chunk 161 optimal weight: 5.9990 chunk 334 optimal weight: 4.9990 chunk 270 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 199 optimal weight: 1.9990 chunk 351 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 ASN B 355 GLN B 669 ASN C 204 ASN C 355 GLN C 566 GLN C 669 ASN D 593 ASN E 489 GLN E 593 ASN E 595 GLN F 75 ASN F 220 ASN F 593 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 36591 Z= 0.185 Angle : 0.529 6.156 49803 Z= 0.284 Chirality : 0.042 0.208 5229 Planarity : 0.004 0.040 6315 Dihedral : 8.261 73.819 6000 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.49 % Allowed : 8.33 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.13), residues: 4062 helix: 1.35 (0.13), residues: 1509 sheet: 0.65 (0.21), residues: 561 loop : 0.71 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 234 HIS 0.003 0.001 HIS C 242 PHE 0.013 0.002 PHE A 531 TYR 0.019 0.001 TYR D 432 ARG 0.003 0.000 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 435 time to evaluate : 4.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7352 (ttm) cc_final: 0.7106 (ttt) REVERT: A 81 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.7050 (mt-10) REVERT: A 122 GLU cc_start: 0.6751 (mp0) cc_final: 0.6505 (mp0) REVERT: A 389 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7595 (mmm160) REVERT: A 597 GLN cc_start: 0.7267 (mt0) cc_final: 0.6984 (mt0) REVERT: B 70 MET cc_start: 0.7237 (ttm) cc_final: 0.6992 (ttt) REVERT: B 81 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.6959 (mt-10) REVERT: B 95 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7375 (mt-10) REVERT: B 525 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6693 (mm-30) REVERT: B 651 ASN cc_start: 0.8525 (p0) cc_final: 0.8291 (p0) REVERT: B 654 PHE cc_start: 0.8378 (m-80) cc_final: 0.8063 (m-80) REVERT: B 683 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.7174 (tm-30) REVERT: C 70 MET cc_start: 0.7242 (ttm) cc_final: 0.6961 (ttt) REVERT: C 386 ASN cc_start: 0.8195 (m110) cc_final: 0.7916 (m-40) REVERT: C 593 LEU cc_start: 0.8222 (tp) cc_final: 0.7956 (tm) REVERT: C 654 PHE cc_start: 0.8343 (m-80) cc_final: 0.8136 (m-80) REVERT: C 683 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7321 (tm-30) REVERT: D 544 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: D 675 ASP cc_start: 0.7761 (m-30) cc_final: 0.7548 (m-30) REVERT: E 20 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8018 (tt) REVERT: E 95 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7491 (mt0) REVERT: F 25 VAL cc_start: 0.7552 (OUTLIER) cc_final: 0.7159 (t) REVERT: F 54 ASP cc_start: 0.7519 (m-30) cc_final: 0.7300 (m-30) REVERT: F 75 ASN cc_start: 0.6697 (OUTLIER) cc_final: 0.6437 (t0) REVERT: F 109 ARG cc_start: 0.7624 (ttm170) cc_final: 0.7262 (mtp-110) REVERT: F 204 ASN cc_start: 0.6681 (t0) cc_final: 0.6395 (t0) outliers start: 55 outliers final: 17 residues processed: 466 average time/residue: 2.9485 time to fit residues: 1669.2136 Evaluate side-chains 457 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 429 time to evaluate : 4.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 683 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 87 LYS Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 75 ASN Chi-restraints excluded: chain F residue 615 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 131 optimal weight: 7.9990 chunk 352 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 229 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 391 optimal weight: 0.0970 chunk 325 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 129 optimal weight: 0.7980 chunk 205 optimal weight: 10.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN A 669 ASN B 355 GLN B 669 ASN C 204 ASN C 355 GLN C 566 GLN C 669 ASN D 204 ASN D 593 ASN E 489 GLN E 593 ASN F 593 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 36591 Z= 0.156 Angle : 0.502 5.881 49803 Z= 0.268 Chirality : 0.041 0.224 5229 Planarity : 0.004 0.037 6315 Dihedral : 7.883 71.343 6000 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.08 % Allowed : 8.82 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.13), residues: 4062 helix: 1.46 (0.13), residues: 1509 sheet: 0.72 (0.21), residues: 561 loop : 0.75 (0.14), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 234 HIS 0.003 0.001 HIS B 242 PHE 0.011 0.001 PHE A 531 TYR 0.016 0.001 TYR B 434 ARG 0.003 0.000 ARG E 297 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 435 time to evaluate : 4.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7345 (ttm) cc_final: 0.6973 (ttt) REVERT: A 81 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7058 (mt-10) REVERT: A 122 GLU cc_start: 0.6770 (mp0) cc_final: 0.6505 (mp0) REVERT: A 389 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7566 (mmm160) REVERT: A 597 GLN cc_start: 0.7189 (mt0) cc_final: 0.6895 (mt0) REVERT: A 683 GLU cc_start: 0.7575 (OUTLIER) cc_final: 0.7026 (tm-30) REVERT: B 70 MET cc_start: 0.7228 (ttm) cc_final: 0.6983 (ttt) REVERT: B 95 GLU cc_start: 0.7631 (mt-10) cc_final: 0.7329 (mt-10) REVERT: B 525 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6691 (mm-30) REVERT: B 651 ASN cc_start: 0.8518 (p0) cc_final: 0.8290 (p0) REVERT: B 654 PHE cc_start: 0.8384 (m-80) cc_final: 0.8065 (m-80) REVERT: B 683 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.7155 (tm-30) REVERT: C 70 MET cc_start: 0.7232 (ttm) cc_final: 0.6952 (ttt) REVERT: C 386 ASN cc_start: 0.8161 (m110) cc_final: 0.7927 (m-40) REVERT: C 593 LEU cc_start: 0.8207 (tp) cc_final: 0.7947 (tm) REVERT: C 654 PHE cc_start: 0.8332 (m-80) cc_final: 0.8124 (m-80) REVERT: C 683 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7319 (tm-30) REVERT: D 43 LEU cc_start: 0.8232 (mp) cc_final: 0.8028 (mp) REVERT: D 544 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7562 (mt-10) REVERT: D 675 ASP cc_start: 0.7765 (m-30) cc_final: 0.7546 (m-30) REVERT: E 20 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8021 (tt) REVERT: E 388 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7344 (mt) REVERT: F 25 VAL cc_start: 0.7473 (OUTLIER) cc_final: 0.7134 (t) REVERT: F 54 ASP cc_start: 0.7519 (m-30) cc_final: 0.7312 (m-30) REVERT: F 109 ARG cc_start: 0.7653 (ttm170) cc_final: 0.7299 (mtp-110) REVERT: F 204 ASN cc_start: 0.6668 (t0) cc_final: 0.6389 (t0) outliers start: 40 outliers final: 16 residues processed: 456 average time/residue: 2.7734 time to fit residues: 1522.5770 Evaluate side-chains 442 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 416 time to evaluate : 4.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 683 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 283 SER Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 377 optimal weight: 3.9990 chunk 44 optimal weight: 10.0000 chunk 223 optimal weight: 6.9990 chunk 286 optimal weight: 4.9990 chunk 221 optimal weight: 2.9990 chunk 329 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 390 optimal weight: 8.9990 chunk 244 optimal weight: 2.9990 chunk 237 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 669 ASN B 204 ASN B 355 GLN B 669 ASN C 204 ASN C 355 GLN C 566 GLN C 669 ASN D 204 ASN D 593 ASN E 204 ASN E 489 GLN E 593 ASN F 75 ASN F 593 ASN F 595 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 36591 Z= 0.247 Angle : 0.579 6.612 49803 Z= 0.313 Chirality : 0.044 0.229 5229 Planarity : 0.004 0.042 6315 Dihedral : 8.372 77.407 6000 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.19 % Allowed : 9.23 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.13), residues: 4062 helix: 1.30 (0.13), residues: 1506 sheet: 0.63 (0.21), residues: 561 loop : 0.66 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 234 HIS 0.003 0.001 HIS F 309 PHE 0.019 0.002 PHE A 531 TYR 0.023 0.002 TYR D 432 ARG 0.004 0.001 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 410 time to evaluate : 4.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7364 (ttm) cc_final: 0.7007 (ttt) REVERT: A 81 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.7035 (mt-10) REVERT: A 389 ARG cc_start: 0.8014 (OUTLIER) cc_final: 0.7578 (mmm160) REVERT: A 597 GLN cc_start: 0.7313 (mt0) cc_final: 0.7030 (mt0) REVERT: A 683 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7120 (tm-30) REVERT: B 70 MET cc_start: 0.7251 (ttm) cc_final: 0.7007 (ttt) REVERT: B 95 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7314 (mt-10) REVERT: B 467 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7937 (mtpp) REVERT: B 525 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6713 (mm-30) REVERT: B 651 ASN cc_start: 0.8534 (p0) cc_final: 0.8307 (p0) REVERT: B 683 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7180 (tm-30) REVERT: C 70 MET cc_start: 0.7270 (ttm) cc_final: 0.7004 (ttt) REVERT: C 386 ASN cc_start: 0.8209 (m110) cc_final: 0.7929 (m-40) REVERT: C 593 LEU cc_start: 0.8220 (tp) cc_final: 0.7952 (tm) REVERT: C 683 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7334 (tm-30) REVERT: D 544 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7602 (mt-10) REVERT: D 675 ASP cc_start: 0.7755 (m-30) cc_final: 0.7533 (m-30) REVERT: E 20 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7939 (tt) REVERT: E 95 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7532 (mt0) REVERT: E 388 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7376 (mt) REVERT: F 25 VAL cc_start: 0.7552 (OUTLIER) cc_final: 0.7258 (t) REVERT: F 109 ARG cc_start: 0.7622 (ttm170) cc_final: 0.7269 (mtp-110) REVERT: F 204 ASN cc_start: 0.6707 (t0) cc_final: 0.6448 (t0) REVERT: F 220 ASN cc_start: 0.7856 (OUTLIER) cc_final: 0.7649 (t0) outliers start: 44 outliers final: 19 residues processed: 436 average time/residue: 2.8427 time to fit residues: 1487.1352 Evaluate side-chains 436 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 404 time to evaluate : 4.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 412 MET Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 467 LYS Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 683 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 109 ARG Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 220 ASN Chi-restraints excluded: chain F residue 615 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 241 optimal weight: 7.9990 chunk 155 optimal weight: 4.9990 chunk 233 optimal weight: 5.9990 chunk 117 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 248 optimal weight: 7.9990 chunk 265 optimal weight: 0.9980 chunk 192 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 306 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN A 669 ASN B 204 ASN B 355 GLN B 669 ASN C 204 ASN C 355 GLN C 566 GLN C 669 ASN D 204 ASN D 593 ASN E 489 GLN E 564 GLN E 593 ASN F 593 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 36591 Z= 0.218 Angle : 0.559 6.451 49803 Z= 0.302 Chirality : 0.043 0.243 5229 Planarity : 0.004 0.040 6315 Dihedral : 8.177 76.603 6000 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.24 % Allowed : 9.44 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.13), residues: 4062 helix: 1.22 (0.13), residues: 1524 sheet: 0.62 (0.21), residues: 561 loop : 0.68 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 234 HIS 0.003 0.001 HIS D 242 PHE 0.015 0.002 PHE A 531 TYR 0.022 0.002 TYR D 432 ARG 0.004 0.000 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 413 time to evaluate : 4.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7370 (ttm) cc_final: 0.7023 (ttt) REVERT: A 81 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: A 389 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7587 (mmm160) REVERT: A 597 GLN cc_start: 0.7338 (mt0) cc_final: 0.7042 (mt0) REVERT: A 683 GLU cc_start: 0.7586 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: B 70 MET cc_start: 0.7259 (ttm) cc_final: 0.7024 (ttt) REVERT: B 81 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6922 (mt-10) REVERT: B 95 GLU cc_start: 0.7638 (mt-10) cc_final: 0.7333 (mt-10) REVERT: B 467 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7901 (mtpp) REVERT: B 525 GLU cc_start: 0.7049 (OUTLIER) cc_final: 0.6718 (mm-30) REVERT: B 651 ASN cc_start: 0.8509 (p0) cc_final: 0.8303 (p0) REVERT: B 683 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7146 (tm-30) REVERT: C 70 MET cc_start: 0.7282 (ttm) cc_final: 0.6916 (ttt) REVERT: C 134 TRP cc_start: 0.8913 (m100) cc_final: 0.8698 (m100) REVERT: C 386 ASN cc_start: 0.8203 (m110) cc_final: 0.7966 (m-40) REVERT: C 593 LEU cc_start: 0.8213 (tp) cc_final: 0.7949 (tm) REVERT: C 683 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7316 (tm-30) REVERT: D 544 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7584 (mt-10) REVERT: D 675 ASP cc_start: 0.7754 (m-30) cc_final: 0.7541 (m-30) REVERT: E 20 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7939 (tt) REVERT: E 95 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7535 (mt0) REVERT: E 388 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7371 (mt) REVERT: F 25 VAL cc_start: 0.7588 (OUTLIER) cc_final: 0.7359 (t) REVERT: F 95 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7620 (mt0) REVERT: F 109 ARG cc_start: 0.7628 (ttm170) cc_final: 0.7273 (mtp-110) REVERT: F 204 ASN cc_start: 0.6668 (t0) cc_final: 0.6430 (t0) outliers start: 46 outliers final: 17 residues processed: 442 average time/residue: 2.9145 time to fit residues: 1542.5505 Evaluate side-chains 441 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 410 time to evaluate : 4.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 467 LYS Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 683 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 283 SER Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 488 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 95 GLN Chi-restraints excluded: chain F residue 615 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 355 optimal weight: 5.9990 chunk 373 optimal weight: 6.9990 chunk 341 optimal weight: 6.9990 chunk 363 optimal weight: 3.9990 chunk 218 optimal weight: 0.6980 chunk 158 optimal weight: 5.9990 chunk 285 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 chunk 328 optimal weight: 6.9990 chunk 344 optimal weight: 3.9990 chunk 362 optimal weight: 4.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN A 669 ASN B 204 ASN B 243 ASN B 355 GLN B 669 ASN C 204 ASN C 355 GLN C 413 ASN C 566 GLN C 669 ASN D 204 ASN D 593 ASN D 595 GLN E 489 GLN E 564 GLN E 593 ASN F 593 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 36591 Z= 0.251 Angle : 0.588 6.766 49803 Z= 0.318 Chirality : 0.044 0.241 5229 Planarity : 0.004 0.042 6315 Dihedral : 8.303 77.945 6000 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.14 % Allowed : 9.69 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.13), residues: 4062 helix: 1.16 (0.13), residues: 1524 sheet: 0.58 (0.21), residues: 561 loop : 0.63 (0.14), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 234 HIS 0.003 0.001 HIS F 309 PHE 0.018 0.002 PHE A 531 TYR 0.023 0.002 TYR D 432 ARG 0.004 0.001 ARG B 276 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 412 time to evaluate : 4.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7369 (ttm) cc_final: 0.7030 (ttt) REVERT: A 81 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7052 (mt-10) REVERT: A 389 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7574 (mmm160) REVERT: A 597 GLN cc_start: 0.7361 (mt0) cc_final: 0.7060 (mt0) REVERT: A 683 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7075 (tm-30) REVERT: B 70 MET cc_start: 0.7258 (ttm) cc_final: 0.7030 (ttt) REVERT: B 81 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.6960 (mt-10) REVERT: B 95 GLU cc_start: 0.7648 (mt-10) cc_final: 0.7351 (mt-10) REVERT: B 467 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7921 (mtpp) REVERT: B 525 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6725 (mm-30) REVERT: B 683 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7136 (tm-30) REVERT: C 70 MET cc_start: 0.7300 (ttm) cc_final: 0.7042 (ttt) REVERT: C 134 TRP cc_start: 0.8901 (m100) cc_final: 0.8667 (m100) REVERT: C 386 ASN cc_start: 0.8220 (m110) cc_final: 0.7958 (m-40) REVERT: C 593 LEU cc_start: 0.8223 (tp) cc_final: 0.7954 (tm) REVERT: C 683 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: D 544 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7614 (mt-10) REVERT: D 675 ASP cc_start: 0.7747 (m-30) cc_final: 0.7526 (m-30) REVERT: E 20 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7932 (tt) REVERT: E 25 VAL cc_start: 0.7631 (OUTLIER) cc_final: 0.7368 (t) REVERT: E 95 GLN cc_start: 0.7909 (OUTLIER) cc_final: 0.7544 (mt0) REVERT: F 95 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7667 (mt0) REVERT: F 109 ARG cc_start: 0.7605 (ttm170) cc_final: 0.7261 (mtp-110) REVERT: F 297 ARG cc_start: 0.6128 (ptt180) cc_final: 0.5732 (mtm-85) outliers start: 42 outliers final: 17 residues processed: 438 average time/residue: 2.9159 time to fit residues: 1542.6012 Evaluate side-chains 437 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 407 time to evaluate : 4.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 GLU Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain A residue 683 GLU Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 467 LYS Chi-restraints excluded: chain B residue 517 ASP Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 683 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 25 VAL Chi-restraints excluded: chain E residue 95 GLN Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 109 ARG Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain E residue 252 GLU Chi-restraints excluded: chain F residue 20 LEU Chi-restraints excluded: chain F residue 95 GLN Chi-restraints excluded: chain F residue 615 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 238 optimal weight: 10.0000 chunk 384 optimal weight: 3.9990 chunk 234 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 267 optimal weight: 1.9990 chunk 403 optimal weight: 0.2980 chunk 371 optimal weight: 7.9990 chunk 321 optimal weight: 6.9990 chunk 33 optimal weight: 0.0010 chunk 248 optimal weight: 8.9990 chunk 197 optimal weight: 2.9990 overall best weight: 1.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN A 669 ASN B 204 ASN B 355 GLN B 669 ASN C 204 ASN C 355 GLN C 566 GLN C 669 ASN D 204 ASN D 593 ASN E 489 GLN E 564 GLN E 593 ASN F 204 ASN F 593 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 36591 Z= 0.158 Angle : 0.514 6.048 49803 Z= 0.275 Chirality : 0.042 0.232 5229 Planarity : 0.004 0.038 6315 Dihedral : 7.696 71.756 6000 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.65 % Allowed : 10.06 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.13), residues: 4062 helix: 1.40 (0.13), residues: 1506 sheet: 0.67 (0.21), residues: 561 loop : 0.73 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 234 HIS 0.003 0.001 HIS B 242 PHE 0.011 0.001 PHE A 531 TYR 0.017 0.001 TYR B 434 ARG 0.002 0.000 ARG D 113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8124 Ramachandran restraints generated. 4062 Oldfield, 0 Emsley, 4062 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 416 time to evaluate : 4.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7372 (ttm) cc_final: 0.7041 (ttt) REVERT: A 389 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.7559 (mmm160) REVERT: A 597 GLN cc_start: 0.7252 (mt0) cc_final: 0.6958 (mt0) REVERT: B 70 MET cc_start: 0.7251 (ttm) cc_final: 0.7024 (ttt) REVERT: B 95 GLU cc_start: 0.7622 (mt-10) cc_final: 0.7317 (mt-10) REVERT: B 467 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7860 (mtpp) REVERT: B 525 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6691 (mm-30) REVERT: B 651 ASN cc_start: 0.8506 (p0) cc_final: 0.8303 (p0) REVERT: C 70 MET cc_start: 0.7294 (ttm) cc_final: 0.6933 (ttt) REVERT: C 134 TRP cc_start: 0.8910 (m100) cc_final: 0.8678 (m100) REVERT: C 386 ASN cc_start: 0.8129 (m110) cc_final: 0.7870 (m-40) REVERT: C 593 LEU cc_start: 0.8201 (tp) cc_final: 0.7945 (tm) REVERT: C 679 TYR cc_start: 0.7482 (m-80) cc_final: 0.7276 (m-80) REVERT: C 683 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: D 544 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7565 (mt-10) REVERT: D 675 ASP cc_start: 0.7729 (m-30) cc_final: 0.7515 (m-30) REVERT: E 20 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7947 (tt) REVERT: F 54 ASP cc_start: 0.7521 (m-30) cc_final: 0.7315 (m-30) REVERT: F 109 ARG cc_start: 0.7611 (ttm170) cc_final: 0.7261 (mtp-110) outliers start: 24 outliers final: 13 residues processed: 431 average time/residue: 2.8544 time to fit residues: 1475.7350 Evaluate side-chains 429 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 410 time to evaluate : 4.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 389 ARG Chi-restraints excluded: chain A residue 467 LYS Chi-restraints excluded: chain B residue 35 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 467 LYS Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 108 VAL Chi-restraints excluded: chain C residue 683 GLU Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 25 VAL Chi-restraints excluded: chain D residue 220 ASN Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain E residue 20 LEU Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 220 ASN Chi-restraints excluded: chain F residue 20 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 255 optimal weight: 5.9990 chunk 342 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 296 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 321 optimal weight: 10.0000 chunk 134 optimal weight: 3.9990 chunk 330 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN A 669 ASN B 204 ASN B 355 GLN B 669 ASN B 686 GLN C 204 ASN C 355 GLN C 566 GLN C 669 ASN D 204 ASN D 593 ASN E 489 GLN E 564 GLN E 593 ASN F 204 ASN F 593 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.122589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.096769 restraints weight = 101728.963| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.30 r_work: 0.2885 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 36591 Z= 0.235 Angle : 0.572 6.650 49803 Z= 0.309 Chirality : 0.043 0.231 5229 Planarity : 0.004 0.041 6315 Dihedral : 8.021 75.872 6000 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.65 % Allowed : 10.25 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.13), residues: 4062 helix: 1.30 (0.13), residues: 1506 sheet: 0.62 (0.21), residues: 561 loop : 0.66 (0.14), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 234 HIS 0.003 0.001 HIS F 309 PHE 0.017 0.002 PHE A 531 TYR 0.022 0.002 TYR D 432 ARG 0.004 0.001 ARG B 276 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23012.46 seconds wall clock time: 396 minutes 33.08 seconds (23793.08 seconds total)