Starting phenix.real_space_refine on Mon Feb 19 22:20:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4n_21042/02_2024/6v4n_21042_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4n_21042/02_2024/6v4n_21042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4n_21042/02_2024/6v4n_21042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4n_21042/02_2024/6v4n_21042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4n_21042/02_2024/6v4n_21042_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v4n_21042/02_2024/6v4n_21042_neut.pdb" } resolution = 2.5 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= 0.007 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: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 164 5.16 5 C 16130 2.51 5 N 4318 2.21 5 O 5250 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I ARG 116": "NH1" <-> "NH2" Residue "I PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 116": "NH1" <-> "NH2" Residue "N ARG 116": "NH1" <-> "NH2" Residue "N PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 116": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25866 Number of models: 1 Model: "" Number of chains: 40 Chain: "I" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3022 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 371} Chain: "M" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3028 Classifications: {'peptide': 391} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 371} Chain: "N" Number of atoms: 3022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 390, 3022 Classifications: {'peptide': 390} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 371} Chain: "W" Number of atoms: 3028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 3028 Classifications: {'peptide': 391} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 371} Chain: "A" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1641 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 203} Chain breaks: 1 Chain: "C" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1641 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 203} Chain breaks: 1 Chain: "D" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1641 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 203} Chain breaks: 1 Chain: "H" Number of atoms: 1641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1641 Classifications: {'peptide': 218} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 203} Chain breaks: 1 Chain: "B" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1648 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "E" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1648 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "G" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1648 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "L" Number of atoms: 1648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1648 Classifications: {'peptide': 213} Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 201} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 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: 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: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 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: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 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: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "X" 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: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' CA': 1, 'BMA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' CA': 1, 'BMA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "M" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "N" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "W" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 36 Classifications: {'water': 36} Link IDs: {None: 35} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 13.97, per 1000 atoms: 0.54 Number of scatterers: 25866 At special positions: 0 Unit cell: (163.9, 163.9, 128.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 164 16.00 O 5250 8.00 N 4318 7.00 C 16130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=48, symmetry=0 Simple disulfide: pdb=" SG CYS I 87 " - pdb=" SG CYS I 420 " distance=1.88 Simple disulfide: pdb=" SG CYS I 122 " - pdb=" SG CYS I 127 " distance=2.03 Simple disulfide: pdb=" SG CYS I 182 " - pdb=" SG CYS I 229 " distance=2.03 Simple disulfide: pdb=" SG CYS I 231 " - pdb=" SG CYS I 236 " distance=2.03 Simple disulfide: pdb=" SG CYS I 277 " - pdb=" SG CYS I 291 " distance=2.03 Simple disulfide: pdb=" SG CYS I 279 " - pdb=" SG CYS I 289 " distance=2.03 Simple disulfide: pdb=" SG CYS I 318 " - pdb=" SG CYS I 337 " distance=2.03 Simple disulfide: pdb=" SG CYS I 424 " - pdb=" SG CYS I 447 " distance=2.03 Simple disulfide: pdb=" SG CYS M 87 " - pdb=" SG CYS M 420 " distance=2.03 Simple disulfide: pdb=" SG CYS M 122 " - pdb=" SG CYS M 127 " distance=2.03 Simple disulfide: pdb=" SG CYS M 182 " - pdb=" SG CYS M 229 " distance=2.03 Simple disulfide: pdb=" SG CYS M 231 " - pdb=" SG CYS M 236 " distance=2.03 Simple disulfide: pdb=" SG CYS M 277 " - pdb=" SG CYS M 291 " distance=2.03 Simple disulfide: pdb=" SG CYS M 279 " - pdb=" SG CYS M 289 " distance=2.03 Simple disulfide: pdb=" SG CYS M 318 " - pdb=" SG CYS M 337 " distance=2.03 Simple disulfide: pdb=" SG CYS M 424 " - pdb=" SG CYS M 447 " distance=2.03 Simple disulfide: pdb=" SG CYS N 87 " - pdb=" SG CYS N 420 " distance=2.04 Simple disulfide: pdb=" SG CYS N 122 " - pdb=" SG CYS N 127 " distance=2.03 Simple disulfide: pdb=" SG CYS N 182 " - pdb=" SG CYS N 229 " distance=2.03 Simple disulfide: pdb=" SG CYS N 231 " - pdb=" SG CYS N 236 " distance=2.03 Simple disulfide: pdb=" SG CYS N 277 " - pdb=" SG CYS N 291 " distance=2.03 Simple disulfide: pdb=" SG CYS N 279 " - pdb=" SG CYS N 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 318 " - pdb=" SG CYS N 337 " distance=2.03 Simple disulfide: pdb=" SG CYS N 424 " - pdb=" SG CYS N 447 " distance=2.03 Simple disulfide: pdb=" SG CYS W 87 " - pdb=" SG CYS W 420 " distance=2.04 Simple disulfide: pdb=" SG CYS W 122 " - pdb=" SG CYS W 127 " distance=2.03 Simple disulfide: pdb=" SG CYS W 182 " - pdb=" SG CYS W 229 " distance=2.03 Simple disulfide: pdb=" SG CYS W 231 " - pdb=" SG CYS W 236 " distance=2.03 Simple disulfide: pdb=" SG CYS W 277 " - pdb=" SG CYS W 291 " distance=2.03 Simple disulfide: pdb=" SG CYS W 279 " - pdb=" SG CYS W 289 " distance=2.03 Simple disulfide: pdb=" SG CYS W 318 " - pdb=" SG CYS W 337 " distance=2.03 Simple disulfide: pdb=" SG CYS W 424 " - pdb=" SG CYS W 447 " distance=2.03 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.04 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 196 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 92 " distance=2.03 Simple disulfide: pdb=" SG CYS C 140 " - pdb=" SG CYS C 196 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.04 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 194 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 194 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA M 508 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG T 2 " - " BMA N 508 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " " NAG X 1 " - " NAG X 2 " " NAG X 2 " - " BMA X 3 " NAG-ASN " NAG F 1 " - " ASN I 144 " " NAG J 1 " - " ASN I 463 " " NAG K 1 " - " ASN I 284 " " NAG O 1 " - " ASN M 144 " " NAG P 1 " - " ASN M 463 " " NAG Q 1 " - " ASN M 284 " " NAG R 1 " - " ASN N 144 " " NAG S 1 " - " ASN N 463 " " NAG T 1 " - " ASN N 284 " " NAG U 1 " - " ASN W 144 " " NAG V 1 " - " ASN W 463 " " NAG X 1 " - " ASN W 284 " Time building additional restraints: 10.26 Conformation dependent library (CDL) restraints added in 4.6 seconds 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5988 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 76 sheets defined 3.6% alpha, 46.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.30 Creating SS restraints... Processing helix chain 'I' and resid 99 through 104 removed outlier: 3.595A pdb=" N GLY I 104 " --> pdb=" O HIS I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 147 removed outlier: 4.704A pdb=" N ARG I 147 " --> pdb=" O ASN I 144 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 103 Processing helix chain 'N' and resid 99 through 103 Processing helix chain 'W' and resid 99 through 103 Processing helix chain 'W' and resid 143 through 147 removed outlier: 4.707A pdb=" N ARG W 147 " --> pdb=" O ASN W 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'D' and resid 63 through 65 No H-bonds generated for 'chain 'D' and resid 63 through 65' Processing helix chain 'D' and resid 187 through 189 No H-bonds generated for 'chain 'D' and resid 187 through 189' Processing helix chain 'H' and resid 63 through 65 No H-bonds generated for 'chain 'H' and resid 63 through 65' Processing helix chain 'H' and resid 187 through 189 No H-bonds generated for 'chain 'H' and resid 187 through 189' Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 182 through 189 removed outlier: 4.206A pdb=" N HIS B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 128 Processing helix chain 'E' and resid 182 through 189 removed outlier: 4.205A pdb=" N HIS E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 128 Processing helix chain 'G' and resid 182 through 189 removed outlier: 4.206A pdb=" N HIS G 189 " --> pdb=" O ASP G 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 182 through 189 removed outlier: 4.205A pdb=" N HIS L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 92 through 98 removed outlier: 5.438A pdb=" N LYS I 94 " --> pdb=" O CYS I 447 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N CYS I 447 " --> pdb=" O LYS I 94 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU I 96 " --> pdb=" O ILE I 445 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER I 440 " --> pdb=" O HIS I 431 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 113 through 122 removed outlier: 4.840A pdb=" N LEU I 113 " --> pdb=" O ALA I 136 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA I 136 " --> pdb=" O LEU I 113 " (cutoff:3.500A) removed outlier: 8.106A pdb=" N ILE I 115 " --> pdb=" O HIS I 134 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N HIS I 134 " --> pdb=" O ILE I 115 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLU I 117 " --> pdb=" O LEU I 132 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU I 132 " --> pdb=" O GLU I 117 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU I 156 " --> pdb=" O HIS I 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 178 through 183 removed outlier: 3.710A pdb=" N SER I 178 " --> pdb=" O VAL I 193 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU I 202 " --> pdb=" O THR I 213 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR I 213 " --> pdb=" O LEU I 202 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE I 204 " --> pdb=" O THR I 211 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA I 209 " --> pdb=" O TYR I 206 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 222 through 224 Processing sheet with id=AA5, first strand: chain 'I' and resid 222 through 224 removed outlier: 3.975A pdb=" N ASP I 242 " --> pdb=" O GLU I 250 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLU I 250 " --> pdb=" O ASP I 242 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS I 263 " --> pdb=" O LYS I 255 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG I 257 " --> pdb=" O ILE I 261 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ILE I 261 " --> pdb=" O ARG I 257 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 268 through 269 removed outlier: 6.512A pdb=" N THR I 268 " --> pdb=" O ILE I 314 " (cutoff:3.500A) removed outlier: 8.765A pdb=" N LEU I 316 " --> pdb=" O THR I 268 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG I 292 " --> pdb=" O GLU I 276 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N GLU I 276 " --> pdb=" O ARG I 292 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 352 through 356 removed outlier: 7.931A pdb=" N MET I 375 " --> pdb=" O VAL I 401 " (cutoff:3.500A) removed outlier: 8.241A pdb=" N VAL I 401 " --> pdb=" O MET I 375 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N MET I 377 " --> pdb=" O VAL I 399 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N VAL I 399 " --> pdb=" O MET I 377 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEU I 379 " --> pdb=" O SER I 397 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 92 through 98 removed outlier: 5.416A pdb=" N LYS M 94 " --> pdb=" O CYS M 447 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N CYS M 447 " --> pdb=" O LYS M 94 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU M 96 " --> pdb=" O ILE M 445 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER M 440 " --> pdb=" O HIS M 431 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 113 through 122 removed outlier: 4.852A pdb=" N LEU M 113 " --> pdb=" O ALA M 136 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N ALA M 136 " --> pdb=" O LEU M 113 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ILE M 115 " --> pdb=" O HIS M 134 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N HIS M 134 " --> pdb=" O ILE M 115 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N GLU M 117 " --> pdb=" O LEU M 132 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU M 132 " --> pdb=" O GLU M 117 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU M 156 " --> pdb=" O HIS M 173 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 178 through 183 removed outlier: 3.706A pdb=" N SER M 178 " --> pdb=" O VAL M 193 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LEU M 202 " --> pdb=" O THR M 213 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N THR M 213 " --> pdb=" O LEU M 202 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE M 204 " --> pdb=" O THR M 211 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA M 209 " --> pdb=" O TYR M 206 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 222 through 224 removed outlier: 3.544A pdb=" N ASN M 230 " --> pdb=" O TYR M 237 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 222 through 224 removed outlier: 3.970A pdb=" N ASP M 242 " --> pdb=" O GLU M 250 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU M 250 " --> pdb=" O ASP M 242 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LYS M 263 " --> pdb=" O LYS M 255 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ARG M 257 " --> pdb=" O ILE M 261 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ILE M 261 " --> pdb=" O ARG M 257 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 268 through 269 removed outlier: 6.509A pdb=" N THR M 268 " --> pdb=" O ILE M 314 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N LEU M 316 " --> pdb=" O THR M 268 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG M 292 " --> pdb=" O GLU M 276 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N GLU M 276 " --> pdb=" O ARG M 292 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'M' and resid 352 through 356 removed outlier: 7.926A pdb=" N MET M 375 " --> pdb=" O VAL M 401 " (cutoff:3.500A) removed outlier: 8.238A pdb=" N VAL M 401 " --> pdb=" O MET M 375 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N MET M 377 " --> pdb=" O VAL M 399 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N VAL M 399 " --> pdb=" O MET M 377 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N LEU M 379 " --> pdb=" O SER M 397 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'N' and resid 92 through 98 removed outlier: 5.472A pdb=" N LYS N 94 " --> pdb=" O CYS N 447 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N CYS N 447 " --> pdb=" O LYS N 94 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU N 96 " --> pdb=" O ILE N 445 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER N 440 " --> pdb=" O HIS N 431 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'N' and resid 113 through 122 removed outlier: 4.864A pdb=" N LEU N 113 " --> pdb=" O ALA N 136 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ALA N 136 " --> pdb=" O LEU N 113 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE N 115 " --> pdb=" O HIS N 134 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N HIS N 134 " --> pdb=" O ILE N 115 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N GLU N 117 " --> pdb=" O LEU N 132 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU N 132 " --> pdb=" O GLU N 117 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU N 156 " --> pdb=" O HIS N 173 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 178 through 183 removed outlier: 3.705A pdb=" N SER N 178 " --> pdb=" O VAL N 193 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU N 202 " --> pdb=" O THR N 213 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR N 213 " --> pdb=" O LEU N 202 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ILE N 204 " --> pdb=" O THR N 211 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA N 209 " --> pdb=" O TYR N 206 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 222 through 224 removed outlier: 3.546A pdb=" N ASN N 230 " --> pdb=" O TYR N 237 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 222 through 224 removed outlier: 3.980A pdb=" N ASP N 242 " --> pdb=" O GLU N 250 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLU N 250 " --> pdb=" O ASP N 242 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS N 263 " --> pdb=" O LYS N 255 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ARG N 257 " --> pdb=" O ILE N 261 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ILE N 261 " --> pdb=" O ARG N 257 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 268 through 269 removed outlier: 6.497A pdb=" N THR N 268 " --> pdb=" O ILE N 314 " (cutoff:3.500A) removed outlier: 8.758A pdb=" N LEU N 316 " --> pdb=" O THR N 268 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ARG N 292 " --> pdb=" O GLU N 276 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N GLU N 276 " --> pdb=" O ARG N 292 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 352 through 356 removed outlier: 7.929A pdb=" N MET N 375 " --> pdb=" O VAL N 401 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N VAL N 401 " --> pdb=" O MET N 375 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N MET N 377 " --> pdb=" O VAL N 399 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL N 399 " --> pdb=" O MET N 377 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU N 379 " --> pdb=" O SER N 397 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'W' and resid 92 through 98 removed outlier: 5.431A pdb=" N LYS W 94 " --> pdb=" O CYS W 447 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N CYS W 447 " --> pdb=" O LYS W 94 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU W 96 " --> pdb=" O ILE W 445 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER W 440 " --> pdb=" O HIS W 431 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'W' and resid 113 through 122 removed outlier: 4.849A pdb=" N LEU W 113 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA W 136 " --> pdb=" O LEU W 113 " (cutoff:3.500A) removed outlier: 8.104A pdb=" N ILE W 115 " --> pdb=" O HIS W 134 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N HIS W 134 " --> pdb=" O ILE W 115 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N GLU W 117 " --> pdb=" O LEU W 132 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LEU W 132 " --> pdb=" O GLU W 117 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N LEU W 156 " --> pdb=" O HIS W 173 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'W' and resid 178 through 183 removed outlier: 3.736A pdb=" N SER W 178 " --> pdb=" O VAL W 193 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU W 202 " --> pdb=" O THR W 213 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N THR W 213 " --> pdb=" O LEU W 202 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE W 204 " --> pdb=" O THR W 211 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA W 209 " --> pdb=" O TYR W 206 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'W' and resid 222 through 224 Processing sheet with id=AC8, first strand: chain 'W' and resid 222 through 224 removed outlier: 3.963A pdb=" N ASP W 242 " --> pdb=" O GLU W 250 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU W 250 " --> pdb=" O ASP W 242 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS W 263 " --> pdb=" O LYS W 255 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG W 257 " --> pdb=" O ILE W 261 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ILE W 261 " --> pdb=" O ARG W 257 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'W' and resid 268 through 269 removed outlier: 6.513A pdb=" N THR W 268 " --> pdb=" O ILE W 314 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N LEU W 316 " --> pdb=" O THR W 268 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG W 292 " --> pdb=" O GLU W 276 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N GLU W 276 " --> pdb=" O ARG W 292 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'W' and resid 352 through 356 removed outlier: 7.937A pdb=" N MET W 375 " --> pdb=" O VAL W 401 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N VAL W 401 " --> pdb=" O MET W 375 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N MET W 377 " --> pdb=" O VAL W 399 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N VAL W 399 " --> pdb=" O MET W 377 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU W 379 " --> pdb=" O SER W 397 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AD3, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.947A pdb=" N TYR A 33 " --> pdb=" O GLY A 95 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP A 34 " --> pdb=" O TYR A 50 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N TYR A 50 " --> pdb=" O TRP A 34 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP A 36 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.903A pdb=" N VAL A 102 " --> pdb=" O ARG A 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP A 96 " --> pdb=" O MET A 100I" (cutoff:3.500A) removed outlier: 5.385A pdb=" N MET A 100I" --> pdb=" O ASP A 96 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 120 through 124 removed outlier: 4.883A pdb=" N ALA A 137 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A 184 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLY A 139 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL A 182 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU A 141 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER A 180 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS A 143 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU A 178 " --> pdb=" O LYS A 143 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL A 181 " --> pdb=" O HIS A 164 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 120 through 124 removed outlier: 4.883A pdb=" N ALA A 137 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL A 184 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLY A 139 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL A 182 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LEU A 141 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER A 180 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS A 143 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU A 178 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 151 through 154 Processing sheet with id=AD8, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.948A pdb=" N TYR C 33 " --> pdb=" O GLY C 95 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TRP C 34 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR C 50 " --> pdb=" O TRP C 34 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.903A pdb=" N VAL C 102 " --> pdb=" O ARG C 94 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP C 96 " --> pdb=" O MET C 100I" (cutoff:3.500A) removed outlier: 5.385A pdb=" N MET C 100I" --> pdb=" O ASP C 96 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 120 through 124 removed outlier: 4.883A pdb=" N ALA C 137 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C 184 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLY C 139 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL C 182 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU C 141 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N SER C 180 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS C 143 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU C 178 " --> pdb=" O LYS C 143 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL C 181 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 120 through 124 removed outlier: 4.883A pdb=" N ALA C 137 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL C 184 " --> pdb=" O ALA C 137 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLY C 139 " --> pdb=" O VAL C 182 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL C 182 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU C 141 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N SER C 180 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS C 143 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU C 178 " --> pdb=" O LYS C 143 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 151 through 154 Processing sheet with id=AE5, first strand: chain 'D' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.947A pdb=" N TYR D 33 " --> pdb=" O GLY D 95 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR D 50 " --> pdb=" O TRP D 34 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.903A pdb=" N VAL D 102 " --> pdb=" O ARG D 94 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ASP D 96 " --> pdb=" O MET D 100I" (cutoff:3.500A) removed outlier: 5.384A pdb=" N MET D 100I" --> pdb=" O ASP D 96 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 120 through 124 removed outlier: 4.882A pdb=" N ALA D 137 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL D 184 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLY D 139 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL D 182 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU D 141 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER D 180 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS D 143 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU D 178 " --> pdb=" O LYS D 143 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL D 181 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 120 through 124 removed outlier: 4.882A pdb=" N ALA D 137 " --> pdb=" O VAL D 184 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL D 184 " --> pdb=" O ALA D 137 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N GLY D 139 " --> pdb=" O VAL D 182 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL D 182 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU D 141 " --> pdb=" O SER D 180 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER D 180 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS D 143 " --> pdb=" O LEU D 178 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU D 178 " --> pdb=" O LYS D 143 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 151 through 154 Processing sheet with id=AF2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.947A pdb=" N TYR H 33 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TRP H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N TYR H 50 " --> pdb=" O TRP H 34 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.905A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASP H 96 " --> pdb=" O MET H 100I" (cutoff:3.500A) removed outlier: 5.385A pdb=" N MET H 100I" --> pdb=" O ASP H 96 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'H' and resid 120 through 124 removed outlier: 4.882A pdb=" N ALA H 137 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL H 184 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLY H 139 " --> pdb=" O VAL H 182 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL H 182 " --> pdb=" O GLY H 139 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU H 141 " --> pdb=" O SER H 180 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER H 180 " --> pdb=" O LEU H 141 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS H 143 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU H 178 " --> pdb=" O LYS H 143 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL H 181 " --> pdb=" O HIS H 164 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 120 through 124 removed outlier: 4.882A pdb=" N ALA H 137 " --> pdb=" O VAL H 184 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL H 184 " --> pdb=" O ALA H 137 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N GLY H 139 " --> pdb=" O VAL H 182 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N VAL H 182 " --> pdb=" O GLY H 139 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU H 141 " --> pdb=" O SER H 180 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N SER H 180 " --> pdb=" O LEU H 141 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N LYS H 143 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU H 178 " --> pdb=" O LYS H 143 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 151 through 154 Processing sheet with id=AF8, first strand: chain 'B' and resid 4 through 7 removed outlier: 12.098A pdb=" N CYS B 23 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 11.080A pdb=" N THR B 74 " --> pdb=" O CYS B 23 " (cutoff:3.500A) removed outlier: 11.922A pdb=" N ALA B 25 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 11.843A pdb=" N THR B 72 " --> pdb=" O ALA B 25 " (cutoff:3.500A) removed outlier: 11.444A pdb=" N GLN B 27 " --> pdb=" O ASP B 70 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP B 70 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'B' and resid 12 through 13 Processing sheet with id=AG1, first strand: chain 'B' and resid 53 through 54 removed outlier: 5.603A pdb=" N LEU B 46 " --> pdb=" O GLN B 37 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN B 37 " --> pdb=" O LEU B 46 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 48 " --> pdb=" O TRP B 35 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 97 " --> pdb=" O GLN B 90 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'B' and resid 115 through 116 removed outlier: 5.856A pdb=" N LEU B 135 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N SER B 177 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASN B 137 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU B 175 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA B 130 " --> pdb=" O LEU B 181 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'B' and resid 115 through 116 removed outlier: 5.856A pdb=" N LEU B 135 " --> pdb=" O SER B 177 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N SER B 177 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASN B 137 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU B 175 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR B 178 " --> pdb=" O GLN B 160 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'B' and resid 153 through 155 removed outlier: 3.511A pdb=" N VAL B 150 " --> pdb=" O ALA B 153 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TRP B 148 " --> pdb=" O GLN B 155 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 4 through 7 removed outlier: 12.098A pdb=" N CYS E 23 " --> pdb=" O THR E 74 " (cutoff:3.500A) removed outlier: 11.081A pdb=" N THR E 74 " --> pdb=" O CYS E 23 " (cutoff:3.500A) removed outlier: 11.922A pdb=" N ALA E 25 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N THR E 72 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 11.445A pdb=" N GLN E 27 " --> pdb=" O ASP E 70 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP E 70 " --> pdb=" O GLN E 27 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 12 through 13 Processing sheet with id=AG7, first strand: chain 'E' and resid 53 through 54 removed outlier: 5.602A pdb=" N LEU E 46 " --> pdb=" O GLN E 37 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN E 37 " --> pdb=" O LEU E 46 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE E 48 " --> pdb=" O TRP E 35 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR E 97 " --> pdb=" O GLN E 90 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 115 through 116 removed outlier: 5.857A pdb=" N LEU E 135 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N SER E 177 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASN E 137 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU E 175 " --> pdb=" O ASN E 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA E 130 " --> pdb=" O LEU E 181 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'E' and resid 115 through 116 removed outlier: 5.857A pdb=" N LEU E 135 " --> pdb=" O SER E 177 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N SER E 177 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASN E 137 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU E 175 " --> pdb=" O ASN E 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR E 178 " --> pdb=" O GLN E 160 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 153 through 155 removed outlier: 3.510A pdb=" N VAL E 150 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N TRP E 148 " --> pdb=" O GLN E 155 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 4 through 7 removed outlier: 12.097A pdb=" N CYS G 23 " --> pdb=" O THR G 74 " (cutoff:3.500A) removed outlier: 11.081A pdb=" N THR G 74 " --> pdb=" O CYS G 23 " (cutoff:3.500A) removed outlier: 11.922A pdb=" N ALA G 25 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N THR G 72 " --> pdb=" O ALA G 25 " (cutoff:3.500A) removed outlier: 11.444A pdb=" N GLN G 27 " --> pdb=" O ASP G 70 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ASP G 70 " --> pdb=" O GLN G 27 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 12 through 13 Processing sheet with id=AH4, first strand: chain 'G' and resid 53 through 54 removed outlier: 5.603A pdb=" N LEU G 46 " --> pdb=" O GLN G 37 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N GLN G 37 " --> pdb=" O LEU G 46 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE G 48 " --> pdb=" O TRP G 35 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N THR G 97 " --> pdb=" O GLN G 90 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 115 through 116 removed outlier: 5.857A pdb=" N LEU G 135 " --> pdb=" O SER G 177 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N SER G 177 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASN G 137 " --> pdb=" O LEU G 175 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU G 175 " --> pdb=" O ASN G 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA G 130 " --> pdb=" O LEU G 181 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 115 through 116 removed outlier: 5.857A pdb=" N LEU G 135 " --> pdb=" O SER G 177 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N SER G 177 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASN G 137 " --> pdb=" O LEU G 175 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU G 175 " --> pdb=" O ASN G 137 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N THR G 178 " --> pdb=" O GLN G 160 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 153 through 155 removed outlier: 3.511A pdb=" N VAL G 150 " --> pdb=" O ALA G 153 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TRP G 148 " --> pdb=" O GLN G 155 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'L' and resid 4 through 7 removed outlier: 12.098A pdb=" N CYS L 23 " --> pdb=" O THR L 74 " (cutoff:3.500A) removed outlier: 11.082A pdb=" N THR L 74 " --> pdb=" O CYS L 23 " (cutoff:3.500A) removed outlier: 11.923A pdb=" N ALA L 25 " --> pdb=" O THR L 72 " (cutoff:3.500A) removed outlier: 11.844A pdb=" N THR L 72 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 11.445A pdb=" N GLN L 27 " --> pdb=" O ASP L 70 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N ASP L 70 " --> pdb=" O GLN L 27 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'L' and resid 12 through 13 Processing sheet with id=AI1, first strand: chain 'L' and resid 53 through 54 removed outlier: 5.602A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE L 48 " --> pdb=" O TRP L 35 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'L' and resid 115 through 116 removed outlier: 5.856A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA L 130 " --> pdb=" O LEU L 181 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 115 through 116 removed outlier: 5.856A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THR L 178 " --> pdb=" O GLN L 160 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'L' and resid 153 through 155 removed outlier: 3.511A pdb=" N VAL L 150 " --> pdb=" O ALA L 153 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TRP L 148 " --> pdb=" O GLN L 155 " (cutoff:3.500A) 824 hydrogen bonds defined for protein. 2079 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: 10.23 Time building geometry restraints manager: 11.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8176 1.34 - 1.47: 6959 1.47 - 1.60: 10916 1.60 - 1.72: 5 1.72 - 1.85: 228 Bond restraints: 26284 Sorted by residual: bond pdb=" C1 NAG R 1 " pdb=" C2 NAG R 1 " ideal model delta sigma weight residual 1.532 1.641 -0.109 2.00e-02 2.50e+03 2.97e+01 bond pdb=" C1 NAG J 1 " pdb=" C2 NAG J 1 " ideal model delta sigma weight residual 1.532 1.638 -0.106 2.00e-02 2.50e+03 2.78e+01 bond pdb=" C1 NAG K 1 " pdb=" C2 NAG K 1 " ideal model delta sigma weight residual 1.532 1.629 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C ASN N 144 " pdb=" N GLY N 145 " ideal model delta sigma weight residual 1.331 1.398 -0.068 1.46e-02 4.69e+03 2.16e+01 bond pdb=" N ASN N 144 " pdb=" CA ASN N 144 " ideal model delta sigma weight residual 1.457 1.412 0.046 1.29e-02 6.01e+03 1.25e+01 ... (remaining 26279 not shown) Histogram of bond angle deviations from ideal: 96.93 - 104.37: 492 104.37 - 111.81: 12810 111.81 - 119.25: 8504 119.25 - 126.69: 13420 126.69 - 134.12: 436 Bond angle restraints: 35662 Sorted by residual: angle pdb=" CA TYR N 143 " pdb=" C TYR N 143 " pdb=" N ASN N 144 " ideal model delta sigma weight residual 117.48 111.23 6.25 1.41e+00 5.03e-01 1.96e+01 angle pdb=" C ASN N 144 " pdb=" N GLY N 145 " pdb=" CA GLY N 145 " ideal model delta sigma weight residual 121.41 129.77 -8.36 1.96e+00 2.60e-01 1.82e+01 angle pdb=" O TYR N 143 " pdb=" C TYR N 143 " pdb=" N ASN N 144 " ideal model delta sigma weight residual 122.23 127.50 -5.27 1.30e+00 5.92e-01 1.64e+01 angle pdb=" N ASP C 100A" pdb=" CA ASP C 100A" pdb=" C ASP C 100A" ideal model delta sigma weight residual 110.80 119.38 -8.58 2.13e+00 2.20e-01 1.62e+01 angle pdb=" N ASP D 100A" pdb=" CA ASP D 100A" pdb=" C ASP D 100A" ideal model delta sigma weight residual 110.80 119.37 -8.57 2.13e+00 2.20e-01 1.62e+01 ... (remaining 35657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.12: 15036 22.12 - 44.23: 900 44.23 - 66.35: 151 66.35 - 88.47: 61 88.47 - 110.59: 32 Dihedral angle restraints: 16180 sinusoidal: 6774 harmonic: 9406 Sorted by residual: dihedral pdb=" CA THR H 191 " pdb=" C THR H 191 " pdb=" N GLN H 192 " pdb=" CA GLN H 192 " ideal model delta harmonic sigma weight residual -180.00 -136.82 -43.18 0 5.00e+00 4.00e-02 7.46e+01 dihedral pdb=" CA THR A 191 " pdb=" C THR A 191 " pdb=" N GLN A 192 " pdb=" CA GLN A 192 " ideal model delta harmonic sigma weight residual -180.00 -136.85 -43.15 0 5.00e+00 4.00e-02 7.45e+01 dihedral pdb=" CA THR D 191 " pdb=" C THR D 191 " pdb=" N GLN D 192 " pdb=" CA GLN D 192 " ideal model delta harmonic sigma weight residual 180.00 -136.85 -43.15 0 5.00e+00 4.00e-02 7.45e+01 ... (remaining 16177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.336: 4009 0.336 - 0.672: 4 0.672 - 1.008: 0 1.008 - 1.344: 2 1.344 - 1.680: 3 Chirality restraints: 4018 Sorted by residual: chirality pdb=" C1 NAG T 2 " pdb=" O4 NAG T 1 " pdb=" C2 NAG T 2 " pdb=" O5 NAG T 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-02 2.50e+03 3.76e+02 chirality pdb=" C1 NAG Q 2 " pdb=" O4 NAG Q 1 " pdb=" C2 NAG Q 2 " pdb=" O5 NAG Q 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-02 2.50e+03 2.84e+02 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-02 2.50e+03 2.33e+02 ... (remaining 4015 not shown) Planarity restraints: 4524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " 0.333 2.00e-02 2.50e+03 2.82e-01 9.97e+02 pdb=" C7 NAG J 1 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " 0.182 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " -0.493 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 1 " -0.212 2.00e-02 2.50e+03 1.81e-01 4.07e+02 pdb=" C7 NAG K 1 " 0.046 2.00e-02 2.50e+03 pdb=" C8 NAG K 1 " 0.035 2.00e-02 2.50e+03 pdb=" N2 NAG K 1 " 0.296 2.00e-02 2.50e+03 pdb=" O7 NAG K 1 " -0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG K 2 " 0.090 2.00e-02 2.50e+03 7.43e-02 6.89e+01 pdb=" C7 NAG K 2 " -0.024 2.00e-02 2.50e+03 pdb=" C8 NAG K 2 " 0.068 2.00e-02 2.50e+03 pdb=" N2 NAG K 2 " -0.118 2.00e-02 2.50e+03 pdb=" O7 NAG K 2 " -0.015 2.00e-02 2.50e+03 ... (remaining 4521 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 297 2.57 - 3.15: 20986 3.15 - 3.74: 37661 3.74 - 4.32: 60018 4.32 - 4.90: 98598 Nonbonded interactions: 217560 Sorted by model distance: nonbonded pdb=" O HOH W 606 " pdb=" O HOH W 630 " model vdw 1.991 2.440 nonbonded pdb=" O HOH M 606 " pdb=" O HOH M 638 " model vdw 1.991 2.440 nonbonded pdb=" O HOH I 608 " pdb=" O HOH I 629 " model vdw 1.991 2.440 nonbonded pdb=" O HOH N 607 " pdb=" O HOH N 636 " model vdw 1.991 2.440 nonbonded pdb=" NH1 ARG W 116 " pdb=" OE2 GLU W 117 " model vdw 2.108 2.520 ... (remaining 217555 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'K' selection = chain 'O' selection = chain 'R' selection = chain 'U' selection = chain 'X' } ncs_group { reference = (chain 'I' and resid 77 through 466) selection = (chain 'M' and resid 77 through 466) selection = (chain 'N' and resid 77 through 466) selection = (chain 'W' and resid 77 through 466) } ncs_group { reference = chain 'J' selection = chain 'P' selection = chain 'Q' selection = chain 'S' selection = chain 'T' selection = chain 'V' } 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=0.05 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: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.970 Check model and map are aligned: 0.380 Set scattering table: 0.220 Process input model: 68.250 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 91.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.109 26284 Z= 0.627 Angle : 0.791 9.272 35662 Z= 0.413 Chirality : 0.074 1.680 4018 Planarity : 0.007 0.282 4512 Dihedral : 16.017 110.586 10048 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.42 % Favored : 93.55 % Rotamer: Outliers : 1.03 % Allowed : 1.71 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.13), residues: 3254 helix: -3.78 (0.49), residues: 64 sheet: -1.35 (0.13), residues: 1316 loop : -2.69 (0.11), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP W 177 HIS 0.006 0.001 HIS M 101 PHE 0.017 0.002 PHE H 91 TYR 0.025 0.002 TYR H 33 ARG 0.007 0.001 ARG M 154 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 331 time to evaluate : 2.698 Fit side-chains REVERT: W 194 ASP cc_start: 0.7386 (p0) cc_final: 0.6900 (p0) REVERT: A 6 GLU cc_start: 0.8797 (mp0) cc_final: 0.8560 (mp0) REVERT: A 27 ASP cc_start: 0.8486 (t0) cc_final: 0.8270 (t70) REVERT: A 96 ASP cc_start: 0.8162 (t0) cc_final: 0.7856 (t0) REVERT: A 180 SER cc_start: 0.6716 (OUTLIER) cc_final: 0.6436 (p) REVERT: C 6 GLU cc_start: 0.8837 (mp0) cc_final: 0.8616 (mp0) REVERT: C 27 ASP cc_start: 0.8590 (t0) cc_final: 0.8334 (t70) REVERT: C 96 ASP cc_start: 0.8107 (t0) cc_final: 0.7745 (t0) REVERT: D 6 GLU cc_start: 0.8853 (mp0) cc_final: 0.8606 (mp0) REVERT: D 27 ASP cc_start: 0.8474 (t0) cc_final: 0.8259 (t70) REVERT: D 96 ASP cc_start: 0.8148 (t0) cc_final: 0.7841 (t0) REVERT: H 6 GLU cc_start: 0.8750 (mp0) cc_final: 0.8513 (mp0) REVERT: H 96 ASP cc_start: 0.8144 (t0) cc_final: 0.7823 (t0) outliers start: 29 outliers final: 9 residues processed: 355 average time/residue: 1.5790 time to fit residues: 637.3206 Evaluate side-chains 254 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 244 time to evaluate : 2.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain A residue 71 LEU Chi-restraints excluded: chain A residue 180 SER Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 273 optimal weight: 10.0000 chunk 245 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 165 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 253 optimal weight: 10.0000 chunk 98 optimal weight: 0.7980 chunk 154 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 294 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 169 ASN N 169 ASN W 169 ASN C 100EGLN D 60 ASN H 100EGLN B 100 GLN ** B 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 GLN G 100 GLN ** G 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 100 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 26284 Z= 0.199 Angle : 0.659 10.197 35662 Z= 0.341 Chirality : 0.048 0.156 4018 Planarity : 0.005 0.051 4512 Dihedral : 10.269 67.521 4225 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.53 % Allowed : 9.03 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.00 (0.13), residues: 3254 helix: -3.52 (0.43), residues: 64 sheet: -0.64 (0.14), residues: 1364 loop : -1.82 (0.13), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 456 HIS 0.007 0.001 HIS M 101 PHE 0.012 0.002 PHE L 209 TYR 0.015 0.002 TYR B 186 ARG 0.006 0.000 ARG E 16 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 250 time to evaluate : 3.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 369 MET cc_start: 0.8132 (mmm) cc_final: 0.7892 (mmm) REVERT: M 135 TYR cc_start: 0.9455 (OUTLIER) cc_final: 0.7238 (m-80) REVERT: M 369 MET cc_start: 0.8143 (mmm) cc_final: 0.7895 (mmm) REVERT: M 414 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7970 (mm-30) REVERT: N 369 MET cc_start: 0.8138 (mmm) cc_final: 0.7878 (mmm) REVERT: N 392 GLU cc_start: 0.7365 (mt-10) cc_final: 0.7055 (mp0) REVERT: N 414 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: W 194 ASP cc_start: 0.8076 (p0) cc_final: 0.7647 (p0) REVERT: W 392 GLU cc_start: 0.7312 (mt-10) cc_final: 0.6985 (mp0) REVERT: A 96 ASP cc_start: 0.8152 (t0) cc_final: 0.7844 (t0) REVERT: C 27 ASP cc_start: 0.8621 (t0) cc_final: 0.8411 (t70) REVERT: C 96 ASP cc_start: 0.8093 (t0) cc_final: 0.7768 (t0) REVERT: D 96 ASP cc_start: 0.8123 (t0) cc_final: 0.7829 (t0) REVERT: H 96 ASP cc_start: 0.8128 (t0) cc_final: 0.7799 (t0) REVERT: E 3 GLN cc_start: 0.7881 (mm110) cc_final: 0.7634 (mm110) outliers start: 43 outliers final: 20 residues processed: 288 average time/residue: 1.4966 time to fit residues: 494.2753 Evaluate side-chains 260 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 237 time to evaluate : 3.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 456 TRP Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 414 GLU Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 414 GLU Chi-restraints excluded: chain N residue 456 TRP Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 456 TRP Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain C residue 71 LEU Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 71 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 163 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 244 optimal weight: 4.9990 chunk 200 optimal weight: 9.9990 chunk 81 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 chunk 318 optimal weight: 20.0000 chunk 262 optimal weight: 6.9990 chunk 292 optimal weight: 7.9990 chunk 100 optimal weight: 6.9990 chunk 236 optimal weight: 0.4980 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 169 ASN I 225 GLN W 225 GLN A 35 ASN C 35 ASN C 100EGLN D 35 ASN H 35 ASN B 138 ASN ** G 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 26284 Z= 0.343 Angle : 0.675 7.423 35662 Z= 0.351 Chirality : 0.048 0.152 4018 Planarity : 0.005 0.055 4512 Dihedral : 7.893 58.485 4222 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.46 % Allowed : 11.85 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.14), residues: 3254 helix: -3.15 (0.47), residues: 64 sheet: -0.23 (0.14), residues: 1372 loop : -1.51 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP N 456 HIS 0.007 0.001 HIS W 101 PHE 0.012 0.002 PHE H 91 TYR 0.023 0.002 TYR I 383 ARG 0.006 0.001 ARG B 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 243 time to evaluate : 2.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 125 LYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7821 (mptp) REVERT: I 414 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.8214 (mt-10) REVERT: M 125 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7760 (mptp) REVERT: M 229 CYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7526 (p) REVERT: M 414 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8141 (mt-10) REVERT: N 229 CYS cc_start: 0.7845 (OUTLIER) cc_final: 0.7548 (p) REVERT: N 392 GLU cc_start: 0.7378 (mt-10) cc_final: 0.7071 (mp0) REVERT: W 194 ASP cc_start: 0.8272 (p0) cc_final: 0.7955 (p0) REVERT: W 414 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8214 (mt-10) REVERT: A 52 TYR cc_start: 0.9250 (OUTLIER) cc_final: 0.8838 (t80) REVERT: A 96 ASP cc_start: 0.8190 (t0) cc_final: 0.7879 (t0) REVERT: C 96 ASP cc_start: 0.8167 (t0) cc_final: 0.7852 (t0) REVERT: D 52 TYR cc_start: 0.9247 (OUTLIER) cc_final: 0.8838 (t80) REVERT: D 96 ASP cc_start: 0.8155 (t0) cc_final: 0.7836 (t0) REVERT: H 96 ASP cc_start: 0.8184 (t0) cc_final: 0.7861 (t0) REVERT: E 3 GLN cc_start: 0.7949 (mm110) cc_final: 0.7725 (mm110) outliers start: 41 outliers final: 17 residues processed: 280 average time/residue: 1.5440 time to fit residues: 494.5884 Evaluate side-chains 255 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 229 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 125 LYS Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 414 GLU Chi-restraints excluded: chain I residue 456 TRP Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 414 GLU Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 135 TYR Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 456 TRP Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 414 GLU Chi-restraints excluded: chain W residue 456 TRP Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 65 SER Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 65 SER Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain D residue 65 SER Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 65 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 291 optimal weight: 1.9990 chunk 221 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 197 optimal weight: 8.9990 chunk 295 optimal weight: 7.9990 chunk 313 optimal weight: 7.9990 chunk 154 optimal weight: 4.9990 chunk 280 optimal weight: 30.0000 chunk 84 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 225 GLN N 225 GLN B 6 GLN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 6 GLN ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 6 GLN G 138 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 26284 Z= 0.299 Angle : 0.636 6.880 35662 Z= 0.331 Chirality : 0.047 0.144 4018 Planarity : 0.005 0.054 4512 Dihedral : 6.941 59.295 4222 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 2.32 % Allowed : 13.53 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % 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: -1.14 (0.14), residues: 3254 helix: -2.92 (0.48), residues: 64 sheet: 0.01 (0.14), residues: 1386 loop : -1.30 (0.13), residues: 1804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 456 HIS 0.007 0.001 HIS M 101 PHE 0.012 0.002 PHE I 119 TYR 0.020 0.002 TYR I 383 ARG 0.008 0.001 ARG G 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 239 time to evaluate : 3.067 Fit side-chains REVERT: I 229 CYS cc_start: 0.8064 (OUTLIER) cc_final: 0.7802 (p) REVERT: I 392 GLU cc_start: 0.7108 (mp0) cc_final: 0.6832 (mp0) REVERT: I 414 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8197 (mm-30) REVERT: M 125 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7836 (mptp) REVERT: M 229 CYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7578 (p) REVERT: N 229 CYS cc_start: 0.7857 (OUTLIER) cc_final: 0.7616 (p) REVERT: N 392 GLU cc_start: 0.7358 (mt-10) cc_final: 0.7058 (mp0) REVERT: W 194 ASP cc_start: 0.8343 (p0) cc_final: 0.8063 (p0) REVERT: W 229 CYS cc_start: 0.8065 (OUTLIER) cc_final: 0.7817 (p) REVERT: A 52 TYR cc_start: 0.9286 (OUTLIER) cc_final: 0.8892 (t80) REVERT: A 96 ASP cc_start: 0.8190 (t0) cc_final: 0.7902 (t0) REVERT: C 96 ASP cc_start: 0.8177 (t0) cc_final: 0.7875 (t0) REVERT: D 72 ASP cc_start: 0.7791 (t0) cc_final: 0.7586 (OUTLIER) REVERT: D 96 ASP cc_start: 0.8225 (t0) cc_final: 0.7920 (t0) REVERT: H 52 TYR cc_start: 0.9284 (OUTLIER) cc_final: 0.8886 (t80) REVERT: H 96 ASP cc_start: 0.8187 (t0) cc_final: 0.7882 (t0) REVERT: B 79 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7761 (mm110) REVERT: E 3 GLN cc_start: 0.7931 (mm110) cc_final: 0.7721 (mm110) REVERT: E 79 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7705 (mm110) REVERT: G 79 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7685 (mm110) REVERT: L 79 GLN cc_start: 0.7993 (OUTLIER) cc_final: 0.7712 (mm110) outliers start: 65 outliers final: 25 residues processed: 290 average time/residue: 1.5139 time to fit residues: 502.7321 Evaluate side-chains 263 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 227 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 414 GLU Chi-restraints excluded: chain I residue 456 TRP Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 135 TYR Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 456 TRP Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 456 TRP Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 260 optimal weight: 20.0000 chunk 177 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 233 optimal weight: 8.9990 chunk 129 optimal weight: 0.9980 chunk 267 optimal weight: 9.9990 chunk 216 optimal weight: 9.9990 chunk 0 optimal weight: 8.9990 chunk 159 optimal weight: 6.9990 chunk 281 optimal weight: 5.9990 chunk 79 optimal weight: 1.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN C 76 ASN D 76 ASN H 76 ASN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 26284 Z= 0.357 Angle : 0.655 6.963 35662 Z= 0.341 Chirality : 0.048 0.152 4018 Planarity : 0.005 0.057 4512 Dihedral : 6.963 59.915 4218 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.36 % Allowed : 13.74 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % 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: -1.05 (0.14), residues: 3254 helix: -2.72 (0.48), residues: 64 sheet: 0.04 (0.14), residues: 1400 loop : -1.23 (0.13), residues: 1790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 456 HIS 0.007 0.001 HIS I 101 PHE 0.011 0.002 PHE I 119 TYR 0.024 0.002 TYR I 383 ARG 0.003 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 228 time to evaluate : 2.905 Fit side-chains revert: symmetry clash REVERT: I 392 GLU cc_start: 0.7103 (mp0) cc_final: 0.6805 (mp0) REVERT: M 125 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7808 (mptp) REVERT: M 229 CYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7576 (p) REVERT: N 229 CYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7595 (p) REVERT: N 392 GLU cc_start: 0.7369 (mt-10) cc_final: 0.7065 (mp0) REVERT: W 229 CYS cc_start: 0.8087 (OUTLIER) cc_final: 0.7785 (p) REVERT: A 52 TYR cc_start: 0.9292 (OUTLIER) cc_final: 0.8871 (t80) REVERT: A 96 ASP cc_start: 0.8236 (t0) cc_final: 0.7955 (t0) REVERT: C 72 ASP cc_start: 0.7731 (t0) cc_final: 0.7510 (OUTLIER) REVERT: C 96 ASP cc_start: 0.8223 (t0) cc_final: 0.7959 (t0) REVERT: D 3 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8319 (mt0) REVERT: D 52 TYR cc_start: 0.9293 (OUTLIER) cc_final: 0.8876 (t80) REVERT: D 72 ASP cc_start: 0.7741 (t0) cc_final: 0.7531 (OUTLIER) REVERT: D 96 ASP cc_start: 0.8208 (t0) cc_final: 0.7928 (t0) REVERT: H 96 ASP cc_start: 0.8229 (t0) cc_final: 0.7965 (t0) REVERT: B 27 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8009 (pt0) REVERT: B 79 GLN cc_start: 0.8022 (OUTLIER) cc_final: 0.7743 (mm110) REVERT: E 3 GLN cc_start: 0.7928 (mm110) cc_final: 0.7677 (mm110) REVERT: E 79 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.7644 (mm110) REVERT: G 79 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7730 (mm110) REVERT: L 27 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.7992 (pt0) outliers start: 66 outliers final: 35 residues processed: 284 average time/residue: 1.4739 time to fit residues: 482.2710 Evaluate side-chains 273 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 228 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 456 TRP Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain M residue 125 LYS Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 135 TYR Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 456 TRP Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 456 TRP Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain G residue 79 GLN Chi-restraints excluded: chain L residue 27 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 105 optimal weight: 5.9990 chunk 282 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 183 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 313 optimal weight: 5.9990 chunk 260 optimal weight: 0.8980 chunk 145 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 103 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 155 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 26284 Z= 0.263 Angle : 0.602 6.808 35662 Z= 0.314 Chirality : 0.045 0.140 4018 Planarity : 0.005 0.050 4512 Dihedral : 6.697 59.992 4218 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.96 % Allowed : 14.42 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % 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: -0.86 (0.14), residues: 3254 helix: -2.29 (0.54), residues: 64 sheet: 0.24 (0.14), residues: 1372 loop : -1.17 (0.13), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP N 456 HIS 0.007 0.001 HIS N 101 PHE 0.011 0.001 PHE I 119 TYR 0.019 0.002 TYR I 383 ARG 0.003 0.000 ARG W 292 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 228 time to evaluate : 3.080 Fit side-chains REVERT: I 229 CYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7779 (p) REVERT: I 392 GLU cc_start: 0.7096 (mp0) cc_final: 0.6789 (mp0) REVERT: M 229 CYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7578 (p) REVERT: N 229 CYS cc_start: 0.7859 (OUTLIER) cc_final: 0.7586 (p) REVERT: N 392 GLU cc_start: 0.7220 (mt-10) cc_final: 0.6940 (mp0) REVERT: W 194 ASP cc_start: 0.8400 (p0) cc_final: 0.8142 (p0) REVERT: W 229 CYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7794 (p) REVERT: A 3 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8284 (mt0) REVERT: A 96 ASP cc_start: 0.8230 (t0) cc_final: 0.7946 (t0) REVERT: A 105 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8659 (mttm) REVERT: C 3 GLN cc_start: 0.8543 (OUTLIER) cc_final: 0.8271 (mt0) REVERT: C 96 ASP cc_start: 0.8216 (t0) cc_final: 0.7953 (t0) REVERT: D 96 ASP cc_start: 0.8231 (t0) cc_final: 0.7949 (t0) REVERT: H 3 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8288 (mt0) REVERT: H 96 ASP cc_start: 0.8218 (t0) cc_final: 0.7957 (t0) REVERT: E 3 GLN cc_start: 0.7916 (mm110) cc_final: 0.7673 (mm110) REVERT: G 79 GLN cc_start: 0.7938 (OUTLIER) cc_final: 0.7653 (mm110) outliers start: 55 outliers final: 34 residues processed: 274 average time/residue: 1.4299 time to fit residues: 452.5508 Evaluate side-chains 269 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 226 time to evaluate : 3.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 456 TRP Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 135 TYR Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 456 TRP Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 456 TRP Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain G residue 79 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 302 optimal weight: 1.9990 chunk 35 optimal weight: 9.9990 chunk 178 optimal weight: 6.9990 chunk 228 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 chunk 263 optimal weight: 1.9990 chunk 175 optimal weight: 0.0470 chunk 312 optimal weight: 6.9990 chunk 195 optimal weight: 3.9990 chunk 190 optimal weight: 30.0000 chunk 144 optimal weight: 4.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 171 GLN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 155 GLN ** L 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 26284 Z= 0.214 Angle : 0.579 6.669 35662 Z= 0.302 Chirality : 0.044 0.139 4018 Planarity : 0.004 0.049 4512 Dihedral : 6.526 59.950 4218 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.93 % Allowed : 14.70 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % 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: -0.75 (0.14), residues: 3254 helix: -2.04 (0.58), residues: 64 sheet: 0.32 (0.14), residues: 1376 loop : -1.10 (0.13), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 456 HIS 0.007 0.001 HIS I 101 PHE 0.011 0.001 PHE I 119 TYR 0.017 0.001 TYR I 383 ARG 0.002 0.000 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 224 time to evaluate : 2.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 125 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7780 (mppt) REVERT: I 392 GLU cc_start: 0.7045 (mp0) cc_final: 0.6801 (mp0) REVERT: N 392 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6928 (mp0) REVERT: W 194 ASP cc_start: 0.8344 (p0) cc_final: 0.8096 (p0) REVERT: A 3 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8282 (mt0) REVERT: A 52 TYR cc_start: 0.9310 (OUTLIER) cc_final: 0.8855 (t80) REVERT: A 96 ASP cc_start: 0.8227 (t0) cc_final: 0.7940 (t0) REVERT: A 105 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8657 (mttm) REVERT: C 96 ASP cc_start: 0.8213 (t0) cc_final: 0.7960 (t0) REVERT: D 3 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8286 (mt0) REVERT: D 96 ASP cc_start: 0.8197 (t0) cc_final: 0.7917 (t0) REVERT: H 3 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.8288 (mt0) REVERT: H 96 ASP cc_start: 0.8217 (t0) cc_final: 0.7964 (t0) REVERT: E 3 GLN cc_start: 0.7925 (mm110) cc_final: 0.7701 (mm110) REVERT: E 27 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8041 (pt0) REVERT: E 79 GLN cc_start: 0.7866 (OUTLIER) cc_final: 0.7590 (mm110) REVERT: G 79 GLN cc_start: 0.7893 (OUTLIER) cc_final: 0.7618 (mm110) outliers start: 54 outliers final: 39 residues processed: 270 average time/residue: 1.4986 time to fit residues: 463.6541 Evaluate side-chains 269 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 221 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 125 LYS Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 456 TRP Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 135 TYR Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 456 TRP Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 353 VAL Chi-restraints excluded: chain W residue 456 TRP Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain G residue 79 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 193 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 186 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 198 optimal weight: 0.9990 chunk 212 optimal weight: 10.0000 chunk 154 optimal weight: 7.9990 chunk 29 optimal weight: 6.9990 chunk 245 optimal weight: 8.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 225 GLN A 171 GLN C 171 GLN ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 26284 Z= 0.378 Angle : 0.650 6.763 35662 Z= 0.338 Chirality : 0.047 0.139 4018 Planarity : 0.005 0.052 4512 Dihedral : 6.712 59.124 4218 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.43 % Allowed : 14.49 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % 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: -0.78 (0.14), residues: 3254 helix: -2.07 (0.56), residues: 64 sheet: 0.28 (0.14), residues: 1376 loop : -1.10 (0.13), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 34 HIS 0.006 0.001 HIS N 101 PHE 0.012 0.002 PHE N 119 TYR 0.025 0.002 TYR I 383 ARG 0.004 0.001 ARG I 292 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 227 time to evaluate : 2.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: I 125 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7780 (mppt) REVERT: I 239 MET cc_start: 0.8533 (ttp) cc_final: 0.8240 (ttp) REVERT: I 392 GLU cc_start: 0.7109 (mp0) cc_final: 0.6851 (mp0) REVERT: M 229 CYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7566 (p) REVERT: N 229 CYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7580 (p) REVERT: N 392 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7062 (mp0) REVERT: A 3 GLN cc_start: 0.8564 (OUTLIER) cc_final: 0.8294 (mt0) REVERT: A 52 TYR cc_start: 0.9318 (OUTLIER) cc_final: 0.8926 (t80) REVERT: A 96 ASP cc_start: 0.8225 (t0) cc_final: 0.7974 (t0) REVERT: C 3 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8290 (mt0) REVERT: C 72 ASP cc_start: 0.7826 (t0) cc_final: 0.7596 (OUTLIER) REVERT: C 96 ASP cc_start: 0.8214 (t0) cc_final: 0.7991 (t0) REVERT: D 3 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.8301 (mt0) REVERT: D 96 ASP cc_start: 0.8214 (t0) cc_final: 0.7969 (t0) REVERT: H 3 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8302 (mt0) REVERT: H 69 MET cc_start: 0.9202 (mtt) cc_final: 0.8986 (mtt) REVERT: H 96 ASP cc_start: 0.8220 (t0) cc_final: 0.7980 (t0) REVERT: B 79 GLN cc_start: 0.7934 (OUTLIER) cc_final: 0.7645 (mm110) REVERT: E 3 GLN cc_start: 0.7928 (mm110) cc_final: 0.7693 (mm110) REVERT: E 27 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8050 (pt0) REVERT: E 79 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7552 (mm110) outliers start: 68 outliers final: 40 residues processed: 282 average time/residue: 1.4609 time to fit residues: 474.5623 Evaluate side-chains 277 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 227 time to evaluate : 2.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 125 LYS Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 456 TRP Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 135 TYR Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 353 VAL Chi-restraints excluded: chain N residue 456 TRP Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 353 VAL Chi-restraints excluded: chain W residue 456 TRP Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 11 LEU Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 79 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 284 optimal weight: 7.9990 chunk 299 optimal weight: 5.9990 chunk 272 optimal weight: 7.9990 chunk 291 optimal weight: 5.9990 chunk 175 optimal weight: 0.0000 chunk 126 optimal weight: 0.9980 chunk 228 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 chunk 262 optimal weight: 10.0000 chunk 275 optimal weight: 8.9990 chunk 289 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 26284 Z= 0.268 Angle : 0.602 7.726 35662 Z= 0.313 Chirality : 0.045 0.139 4018 Planarity : 0.005 0.050 4512 Dihedral : 6.542 59.350 4218 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.00 % Allowed : 15.13 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % 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: -0.68 (0.14), residues: 3254 helix: -1.92 (0.58), residues: 64 sheet: 0.33 (0.14), residues: 1384 loop : -1.03 (0.14), residues: 1806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP N 456 HIS 0.007 0.001 HIS I 101 PHE 0.011 0.001 PHE I 119 TYR 0.018 0.002 TYR I 383 ARG 0.003 0.000 ARG I 292 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 230 time to evaluate : 2.888 Fit side-chains revert: symmetry clash REVERT: I 125 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7782 (mppt) REVERT: I 229 CYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7820 (p) REVERT: I 239 MET cc_start: 0.8501 (ttp) cc_final: 0.8228 (ttp) REVERT: I 392 GLU cc_start: 0.7086 (mp0) cc_final: 0.6840 (mp0) REVERT: M 229 CYS cc_start: 0.7893 (OUTLIER) cc_final: 0.7593 (p) REVERT: N 392 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6944 (mp0) REVERT: W 229 CYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7785 (p) REVERT: A 3 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.8281 (mt0) REVERT: A 13 ARG cc_start: 0.7914 (mmm160) cc_final: 0.7597 (mmm-85) REVERT: A 52 TYR cc_start: 0.9316 (OUTLIER) cc_final: 0.8911 (t80) REVERT: A 96 ASP cc_start: 0.8241 (t0) cc_final: 0.7975 (t0) REVERT: A 105 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8657 (mttm) REVERT: C 3 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.8264 (mt0) REVERT: C 72 ASP cc_start: 0.7782 (t0) cc_final: 0.7553 (OUTLIER) REVERT: C 96 ASP cc_start: 0.8209 (t0) cc_final: 0.7981 (t0) REVERT: D 3 GLN cc_start: 0.8558 (OUTLIER) cc_final: 0.8290 (mt0) REVERT: D 96 ASP cc_start: 0.8208 (t0) cc_final: 0.7955 (t0) REVERT: H 3 GLN cc_start: 0.8556 (OUTLIER) cc_final: 0.8289 (mt0) REVERT: H 69 MET cc_start: 0.9266 (mtt) cc_final: 0.9037 (mtt) REVERT: H 96 ASP cc_start: 0.8230 (t0) cc_final: 0.7974 (t0) REVERT: B 79 GLN cc_start: 0.7912 (OUTLIER) cc_final: 0.7626 (mm110) REVERT: E 3 GLN cc_start: 0.7905 (mm110) cc_final: 0.7684 (mm110) REVERT: E 27 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8051 (pt0) outliers start: 56 outliers final: 37 residues processed: 277 average time/residue: 1.4589 time to fit residues: 465.7325 Evaluate side-chains 273 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 225 time to evaluate : 2.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 125 LYS Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 353 VAL Chi-restraints excluded: chain I residue 456 TRP Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 353 VAL Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 135 TYR Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 353 VAL Chi-restraints excluded: chain N residue 456 TRP Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 353 VAL Chi-restraints excluded: chain W residue 456 TRP Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 105 LYS Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 11 LEU Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain E residue 27 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 191 optimal weight: 20.0000 chunk 307 optimal weight: 4.9990 chunk 187 optimal weight: 5.9990 chunk 145 optimal weight: 7.9990 chunk 213 optimal weight: 3.9990 chunk 322 optimal weight: 20.0000 chunk 297 optimal weight: 30.0000 chunk 257 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 198 optimal weight: 4.9990 chunk 157 optimal weight: 20.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.140 26284 Z= 0.548 Angle : 0.743 7.759 35662 Z= 0.385 Chirality : 0.052 0.167 4018 Planarity : 0.006 0.055 4512 Dihedral : 6.991 59.737 4218 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.78 % Allowed : 15.49 % Favored : 82.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % 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: -0.78 (0.14), residues: 3254 helix: -1.89 (0.56), residues: 64 sheet: 0.25 (0.14), residues: 1364 loop : -1.08 (0.14), residues: 1826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP C 34 HIS 0.006 0.002 HIS W 101 PHE 0.016 0.002 PHE W 253 TYR 0.030 0.003 TYR I 383 ARG 0.005 0.001 ARG N 292 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6508 Ramachandran restraints generated. 3254 Oldfield, 0 Emsley, 3254 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 226 time to evaluate : 3.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 125 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7749 (mppt) REVERT: I 392 GLU cc_start: 0.7187 (mp0) cc_final: 0.6815 (mp0) REVERT: N 392 GLU cc_start: 0.7372 (mt-10) cc_final: 0.7059 (mp0) REVERT: A 3 GLN cc_start: 0.8581 (OUTLIER) cc_final: 0.8315 (mt0) REVERT: A 13 ARG cc_start: 0.7971 (mmm160) cc_final: 0.7634 (mmm-85) REVERT: A 96 ASP cc_start: 0.8274 (t0) cc_final: 0.8070 (t0) REVERT: A 100 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7982 (mp0) REVERT: C 3 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8298 (mt0) REVERT: C 72 ASP cc_start: 0.7895 (t0) cc_final: 0.7682 (OUTLIER) REVERT: C 100 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7983 (mp0) REVERT: D 3 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.8322 (mt0) REVERT: D 96 ASP cc_start: 0.8244 (t0) cc_final: 0.8041 (t0) REVERT: D 100 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: H 3 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8322 (mt0) REVERT: H 96 ASP cc_start: 0.8263 (t0) cc_final: 0.8057 (t0) REVERT: H 100 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: E 3 GLN cc_start: 0.7905 (mm110) cc_final: 0.7687 (mm110) REVERT: E 27 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.8066 (pt0) outliers start: 50 outliers final: 36 residues processed: 263 average time/residue: 1.4991 time to fit residues: 452.6626 Evaluate side-chains 268 residues out of total 2802 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 223 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 125 LYS Chi-restraints excluded: chain I residue 135 TYR Chi-restraints excluded: chain I residue 229 CYS Chi-restraints excluded: chain I residue 307 VAL Chi-restraints excluded: chain I residue 456 TRP Chi-restraints excluded: chain I residue 458 THR Chi-restraints excluded: chain M residue 135 TYR Chi-restraints excluded: chain M residue 229 CYS Chi-restraints excluded: chain M residue 307 VAL Chi-restraints excluded: chain M residue 456 TRP Chi-restraints excluded: chain N residue 87 CYS Chi-restraints excluded: chain N residue 135 TYR Chi-restraints excluded: chain N residue 229 CYS Chi-restraints excluded: chain N residue 307 VAL Chi-restraints excluded: chain N residue 353 VAL Chi-restraints excluded: chain N residue 456 TRP Chi-restraints excluded: chain W residue 135 TYR Chi-restraints excluded: chain W residue 229 CYS Chi-restraints excluded: chain W residue 307 VAL Chi-restraints excluded: chain W residue 456 TRP Chi-restraints excluded: chain A residue 3 GLN Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 52 TYR Chi-restraints excluded: chain C residue 100 GLU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain D residue 3 GLN Chi-restraints excluded: chain D residue 52 TYR Chi-restraints excluded: chain D residue 100 GLU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 52 TYR Chi-restraints excluded: chain H residue 100 GLU Chi-restraints excluded: chain H residue 100 LEU Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 198 VAL Chi-restraints excluded: chain E residue 27 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 324 random chunks: chunk 204 optimal weight: 0.6980 chunk 273 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 237 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 257 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 264 optimal weight: 5.9990 chunk 32 optimal weight: 4.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.148179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.080828 restraints weight = 28952.795| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.89 r_work: 0.2762 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2639 r_free = 0.2639 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 26284 Z= 0.176 Angle : 0.565 7.458 35662 Z= 0.294 Chirality : 0.044 0.138 4018 Planarity : 0.004 0.048 4512 Dihedral : 6.415 59.460 4218 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.53 % Allowed : 15.77 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.09 % 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: -0.59 (0.14), residues: 3254 helix: -1.62 (0.60), residues: 64 sheet: 0.44 (0.14), residues: 1354 loop : -1.00 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 34 HIS 0.007 0.001 HIS I 101 PHE 0.011 0.001 PHE D 91 TYR 0.012 0.001 TYR I 383 ARG 0.002 0.000 ARG N 292 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9069.21 seconds wall clock time: 162 minutes 41.90 seconds (9761.90 seconds total)