Starting phenix.real_space_refine on Fri Mar 22 17:52:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o81_0649/03_2024/6o81_0649_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o81_0649/03_2024/6o81_0649.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o81_0649/03_2024/6o81_0649.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o81_0649/03_2024/6o81_0649.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o81_0649/03_2024/6o81_0649_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o81_0649/03_2024/6o81_0649_neut_updated.pdb" } resolution = 3.21 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= 0.059 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 S 128 5.16 5 Cl 4 4.86 5 C 21225 2.51 5 N 6093 2.21 5 O 6243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 55": "NH1" <-> "NH2" Residue "A GLU 90": "OE1" <-> "OE2" Residue "A TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 137": "OD1" <-> "OD2" Residue "A ASP 147": "OD1" <-> "OD2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A GLU 187": "OE1" <-> "OE2" Residue "A ASP 199": "OD1" <-> "OD2" Residue "A ASP 206": "OD1" <-> "OD2" Residue "A PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 270": "OD1" <-> "OD2" Residue "A GLU 295": "OE1" <-> "OE2" Residue "A TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 428": "NH1" <-> "NH2" Residue "B ARG 55": "NH1" <-> "NH2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "B TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 137": "OD1" <-> "OD2" Residue "B ASP 147": "OD1" <-> "OD2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 187": "OE1" <-> "OE2" Residue "B ASP 199": "OD1" <-> "OD2" Residue "B ASP 206": "OD1" <-> "OD2" Residue "B PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 270": "OD1" <-> "OD2" Residue "B GLU 295": "OE1" <-> "OE2" Residue "B TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 143": "OE1" <-> "OE2" Residue "C ARG 183": "NH1" <-> "NH2" Residue "C ASP 314": "OD1" <-> "OD2" Residue "C TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D GLU 33": "OE1" <-> "OE2" Residue "D GLU 37": "OE1" <-> "OE2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D GLU 91": "OE1" <-> "OE2" Residue "D GLU 139": "OE1" <-> "OE2" Residue "D GLU 143": "OE1" <-> "OE2" Residue "D GLU 149": "OE1" <-> "OE2" Residue "D ARG 183": "NH1" <-> "NH2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "D GLU 304": "OE1" <-> "OE2" Residue "D ASP 314": "OD1" <-> "OD2" Residue "D TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 321": "NH1" <-> "NH2" Residue "E PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 362": "OD1" <-> "OD2" Residue "E ARG 374": "NH1" <-> "NH2" Residue "E ARG 417": "NH1" <-> "NH2" Residue "E GLU 445": "OE1" <-> "OE2" Residue "E ASP 450": "OD1" <-> "OD2" Residue "E ASP 458": "OD1" <-> "OD2" Residue "E ASP 459": "OD1" <-> "OD2" Residue "E ASP 461": "OD1" <-> "OD2" Residue "E ARG 467": "NH1" <-> "NH2" Residue "E GLU 469": "OE1" <-> "OE2" Residue "E ASP 498": "OD1" <-> "OD2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "F ASP 239": "OD1" <-> "OD2" Residue "F GLU 247": "OE1" <-> "OE2" Residue "F ARG 321": "NH1" <-> "NH2" Residue "F ASP 331": "OD1" <-> "OD2" Residue "F PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 362": "OD1" <-> "OD2" Residue "F ARG 374": "NH1" <-> "NH2" Residue "F ARG 417": "NH1" <-> "NH2" Residue "F ASP 450": "OD1" <-> "OD2" Residue "F ASP 459": "OD1" <-> "OD2" Residue "F ASP 461": "OD1" <-> "OD2" Residue "F ARG 467": "NH1" <-> "NH2" Residue "G GLU 32": "OE1" <-> "OE2" Residue "G PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 46": "NH1" <-> "NH2" Residue "G TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 108": "NH1" <-> "NH2" Residue "G ASP 121": "OD1" <-> "OD2" Residue "G PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 245": "OD1" <-> "OD2" Residue "G PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 299": "OE1" <-> "OE2" Residue "H GLU 32": "OE1" <-> "OE2" Residue "H PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 46": "NH1" <-> "NH2" Residue "H TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 108": "NH1" <-> "NH2" Residue "H ASP 121": "OD1" <-> "OD2" Residue "H PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 245": "OD1" <-> "OD2" Residue "H PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 299": "OE1" <-> "OE2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "I GLU 50": "OE1" <-> "OE2" Residue "I ASP 88": "OD1" <-> "OD2" Residue "I ASP 119": "OD1" <-> "OD2" Residue "I PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 49": "OE1" <-> "OE2" Residue "J GLU 50": "OE1" <-> "OE2" Residue "J ASP 88": "OD1" <-> "OD2" Residue "J ASP 119": "OD1" <-> "OD2" Residue "J PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 42": "OE1" <-> "OE2" Residue "L ARG 56": "NH1" <-> "NH2" Residue "M GLU 42": "OE1" <-> "OE2" Residue "M ARG 56": "NH1" <-> "NH2" Residue "S TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33693 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4055 Classifications: {'peptide': 590} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 177} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 657 Unresolved non-hydrogen angles: 832 Unresolved non-hydrogen dihedrals: 539 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 9, 'GLU:plan': 23, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 391 Chain: "B" Number of atoms: 4055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 590, 4055 Classifications: {'peptide': 590} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 177} Link IDs: {'PCIS': 2, 'PTRANS': 20, 'TRANS': 567} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 657 Unresolved non-hydrogen angles: 832 Unresolved non-hydrogen dihedrals: 539 Unresolved non-hydrogen chiralities: 52 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 10, 'TRP:plan': 2, 'ASP:plan': 11, 'PHE:plan': 9, 'GLU:plan': 23, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 391 Chain: "C" Number of atoms: 2462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2462 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 2472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2472 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 303} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "E" Number of atoms: 2775 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2775 Classifications: {'peptide': 357} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2776 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 338} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2051 Classifications: {'peptide': 285} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 50} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "H" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2051 Classifications: {'peptide': 285} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 50} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 128 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 4, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 71 Chain: "I" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1634 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 9, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 164 Chain: "J" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1634 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 9, 'TRANS': 230} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 376 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 2, 'ASP:plan': 12, 'PHE:plan': 2, 'GLU:plan': 7, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 164 Chain: "L" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1651 Classifications: {'peptide': 275} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 168} Link IDs: {'PTRANS': 9, 'TRANS': 265} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 577 Unresolved non-hydrogen angles: 740 Unresolved non-hydrogen dihedrals: 445 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 25, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 296 Chain: "M" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 1651 Classifications: {'peptide': 275} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 168} Link IDs: {'PTRANS': 9, 'TRANS': 265} Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 577 Unresolved non-hydrogen angles: 740 Unresolved non-hydrogen dihedrals: 445 Unresolved non-hydrogen chiralities: 63 Planarities with less than four sites: {'GLN:plan1': 5, 'ASP:plan': 13, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 25, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 296 Chain: "S" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 2113 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 328} Link IDs: {'PTRANS': 18, 'TRANS': 391} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1054 Unresolved non-hydrogen angles: 1342 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 143 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 14, 'TYR:plan': 6, 'ASN:plan1': 14, 'HIS:plan': 9, 'PHE:plan': 6, 'GLU:plan': 26, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 423 Chain: "T" Number of atoms: 2113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 2113 Classifications: {'peptide': 410} Incomplete info: {'truncation_to_alanine': 328} Link IDs: {'PTRANS': 18, 'TRANS': 391} Chain breaks: 3 Unresolved chain link angles: 18 Unresolved non-hydrogen bonds: 1054 Unresolved non-hydrogen angles: 1342 Unresolved non-hydrogen dihedrals: 832 Unresolved non-hydrogen chiralities: 143 Planarities with less than four sites: {'GLN:plan1': 13, 'ASP:plan': 14, 'TYR:plan': 6, 'ASN:plan1': 14, 'HIS:plan': 9, 'PHE:plan': 6, 'GLU:plan': 26, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 423 Chain: "d" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "e" Number of atoms: 70 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 70 Classifications: {'peptide': 14} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'UNK:plan-1': 14} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 60 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 30 Unusual residues: {'C7B': 1} Classifications: {'undetermined': 1} Conformer: "B" Number of residues, atoms: 1, 30 Unusual residues: {'C7B': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C09AC7B C 401 " occ=0.50 ... (58 atoms not shown) pdb="CL2 BC7B C 401 " occ=0.50 Time building chain proxies: 18.15, per 1000 atoms: 0.54 Number of scatterers: 33693 At special positions: 0 Unit cell: (261.396, 189.06, 124.122, 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) Cl 4 17.00 S 128 16.00 O 6243 8.00 N 6093 7.00 C 21225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.06 Conformation dependent library (CDL) restraints added in 7.3 seconds 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9404 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 171 helices and 50 sheets defined 37.5% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.61 Creating SS restraints... Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 99 through 106 Processing helix chain 'A' and resid 131 through 141 Processing helix chain 'A' and resid 162 through 174 Processing helix chain 'A' and resid 229 through 233 Processing helix chain 'A' and resid 254 through 262 removed outlier: 3.558A pdb=" N ASP A 262 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 278 removed outlier: 3.607A pdb=" N VAL A 278 " --> pdb=" O ARG A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 314 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 550 through 566 Processing helix chain 'A' and resid 571 through 585 Processing helix chain 'A' and resid 589 through 607 Proline residue: A 604 - end of helix Processing helix chain 'A' and resid 614 through 627 Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 629 through 635 Processing helix chain 'A' and resid 639 through 655 Processing helix chain 'A' and resid 657 through 670 removed outlier: 5.200A pdb=" N ILE A 661 " --> pdb=" O ALA A 658 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ALA A 664 " --> pdb=" O ILE A 661 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL A 666 " --> pdb=" O MET A 663 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A 668 " --> pdb=" O LYS A 665 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE A 670 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 686 Processing helix chain 'A' and resid 693 through 698 Processing helix chain 'A' and resid 701 through 714 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 99 through 106 Processing helix chain 'B' and resid 131 through 141 Processing helix chain 'B' and resid 162 through 174 Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 254 through 262 removed outlier: 3.558A pdb=" N ASP B 262 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 278 removed outlier: 3.607A pdb=" N VAL B 278 " --> pdb=" O ARG B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 314 Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 550 through 566 Processing helix chain 'B' and resid 571 through 585 Processing helix chain 'B' and resid 589 through 607 Proline residue: B 604 - end of helix Processing helix chain 'B' and resid 614 through 627 Proline residue: B 623 - end of helix Processing helix chain 'B' and resid 629 through 635 Processing helix chain 'B' and resid 639 through 655 Processing helix chain 'B' and resid 657 through 670 removed outlier: 5.199A pdb=" N ILE B 661 " --> pdb=" O ALA B 658 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA B 664 " --> pdb=" O ILE B 661 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N VAL B 666 " --> pdb=" O MET B 663 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N MET B 668 " --> pdb=" O LYS B 665 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N PHE B 670 " --> pdb=" O LEU B 667 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 686 Processing helix chain 'B' and resid 693 through 698 Processing helix chain 'B' and resid 701 through 714 Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 54 through 71 Processing helix chain 'C' and resid 77 through 97 Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'C' and resid 148 through 157 removed outlier: 4.464A pdb=" N LEU C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 5.680A pdb=" N GLU C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 183 removed outlier: 4.518A pdb=" N ARG C 183 " --> pdb=" O LYS C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 210 removed outlier: 3.562A pdb=" N LYS C 209 " --> pdb=" O VAL C 205 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA C 210 " --> pdb=" O ASN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 225 No H-bonds generated for 'chain 'C' and resid 222 through 225' Processing helix chain 'C' and resid 251 through 260 Processing helix chain 'C' and resid 271 through 273 No H-bonds generated for 'chain 'C' and resid 271 through 273' Processing helix chain 'C' and resid 301 through 303 No H-bonds generated for 'chain 'C' and resid 301 through 303' Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 336 through 343 Processing helix chain 'C' and resid 346 through 349 removed outlier: 3.807A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 346 through 349' Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 31 through 48 removed outlier: 3.598A pdb=" N ASP D 48 " --> pdb=" O GLN D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 54 through 71 removed outlier: 3.517A pdb=" N ARG D 67 " --> pdb=" O ARG D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 97 Processing helix chain 'D' and resid 127 through 145 Processing helix chain 'D' and resid 147 through 157 removed outlier: 4.429A pdb=" N LEU D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLU D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 183 removed outlier: 4.161A pdb=" N ARG D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 207 Processing helix chain 'D' and resid 219 through 226 removed outlier: 3.907A pdb=" N ILE D 222 " --> pdb=" O ASP D 219 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N PHE D 223 " --> pdb=" O ALA D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 301 through 303 No H-bonds generated for 'chain 'D' and resid 301 through 303' Processing helix chain 'D' and resid 318 through 320 No H-bonds generated for 'chain 'D' and resid 318 through 320' Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 348 No H-bonds generated for 'chain 'D' and resid 346 through 348' Processing helix chain 'E' and resid 178 through 180 No H-bonds generated for 'chain 'E' and resid 178 through 180' Processing helix chain 'E' and resid 192 through 195 removed outlier: 3.853A pdb=" N PHE E 195 " --> pdb=" O LEU E 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 192 through 195' Processing helix chain 'E' and resid 205 through 215 Processing helix chain 'E' and resid 222 through 238 Processing helix chain 'E' and resid 248 through 266 removed outlier: 4.763A pdb=" N VAL E 253 " --> pdb=" O SER E 249 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS E 257 " --> pdb=" O VAL E 253 " (cutoff:3.500A) Proline residue: E 258 - end of helix Processing helix chain 'E' and resid 271 through 285 Processing helix chain 'E' and resid 293 through 324 removed outlier: 5.518A pdb=" N ALA E 315 " --> pdb=" O LYS E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 352 Processing helix chain 'E' and resid 369 through 377 Processing helix chain 'E' and resid 391 through 394 No H-bonds generated for 'chain 'E' and resid 391 through 394' Processing helix chain 'E' and resid 421 through 429 Processing helix chain 'E' and resid 440 through 442 No H-bonds generated for 'chain 'E' and resid 440 through 442' Processing helix chain 'E' and resid 460 through 462 No H-bonds generated for 'chain 'E' and resid 460 through 462' Processing helix chain 'E' and resid 509 through 517 Proline residue: E 513 - end of helix Processing helix chain 'F' and resid 178 through 180 No H-bonds generated for 'chain 'F' and resid 178 through 180' Processing helix chain 'F' and resid 192 through 195 Processing helix chain 'F' and resid 205 through 215 Processing helix chain 'F' and resid 222 through 238 Processing helix chain 'F' and resid 248 through 266 removed outlier: 4.665A pdb=" N VAL F 253 " --> pdb=" O SER F 249 " (cutoff:3.500A) Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 271 through 285 Processing helix chain 'F' and resid 293 through 324 removed outlier: 5.462A pdb=" N ALA F 315 " --> pdb=" O LYS F 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 352 Processing helix chain 'F' and resid 369 through 377 Processing helix chain 'F' and resid 391 through 394 No H-bonds generated for 'chain 'F' and resid 391 through 394' Processing helix chain 'F' and resid 421 through 429 Processing helix chain 'F' and resid 440 through 442 No H-bonds generated for 'chain 'F' and resid 440 through 442' Processing helix chain 'F' and resid 460 through 462 No H-bonds generated for 'chain 'F' and resid 460 through 462' Processing helix chain 'F' and resid 509 through 517 Proline residue: F 513 - end of helix Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 22 through 37 Processing helix chain 'G' and resid 43 through 59 WARNING: missing atoms! Processing helix chain 'G' and resid 63 through 82 Processing helix chain 'G' and resid 86 through 105 removed outlier: 4.011A pdb=" N LYS G 91 " --> pdb=" O SER G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 118 removed outlier: 3.705A pdb=" N HIS G 116 " --> pdb=" O ALA G 112 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N THR G 117 " --> pdb=" O ASP G 113 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N PHE G 118 " --> pdb=" O LEU G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 144 Processing helix chain 'G' and resid 161 through 169 Processing helix chain 'G' and resid 212 through 221 Processing helix chain 'G' and resid 232 through 234 No H-bonds generated for 'chain 'G' and resid 232 through 234' Processing helix chain 'G' and resid 278 through 280 No H-bonds generated for 'chain 'G' and resid 278 through 280' Processing helix chain 'G' and resid 295 through 303 Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 22 through 37 Processing helix chain 'H' and resid 43 through 59 WARNING: missing atoms! Processing helix chain 'H' and resid 63 through 82 Processing helix chain 'H' and resid 86 through 105 removed outlier: 4.011A pdb=" N LYS H 91 " --> pdb=" O SER H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 118 removed outlier: 3.705A pdb=" N HIS H 116 " --> pdb=" O ALA H 112 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N THR H 117 " --> pdb=" O ASP H 113 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N PHE H 118 " --> pdb=" O LEU H 114 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 144 Processing helix chain 'H' and resid 161 through 169 Processing helix chain 'H' and resid 212 through 221 Processing helix chain 'H' and resid 232 through 234 No H-bonds generated for 'chain 'H' and resid 232 through 234' Processing helix chain 'H' and resid 278 through 280 No H-bonds generated for 'chain 'H' and resid 278 through 280' Processing helix chain 'H' and resid 295 through 303 Processing helix chain 'I' and resid 35 through 45 Proline residue: I 39 - end of helix Processing helix chain 'I' and resid 63 through 69 removed outlier: 3.846A pdb=" N MET I 69 " --> pdb=" O ALA I 65 " (cutoff:3.500A) Processing helix chain 'I' and resid 86 through 92 Processing helix chain 'I' and resid 94 through 96 No H-bonds generated for 'chain 'I' and resid 94 through 96' Processing helix chain 'I' and resid 115 through 123 Processing helix chain 'I' and resid 184 through 189 Processing helix chain 'I' and resid 209 through 217 Processing helix chain 'I' and resid 224 through 227 No H-bonds generated for 'chain 'I' and resid 224 through 227' Processing helix chain 'I' and resid 230 through 235 Processing helix chain 'I' and resid 282 through 291 removed outlier: 3.996A pdb=" N ARG I 286 " --> pdb=" O TRP I 282 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N TRP I 290 " --> pdb=" O ARG I 286 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 45 Proline residue: J 39 - end of helix Processing helix chain 'J' and resid 63 through 69 removed outlier: 3.846A pdb=" N MET J 69 " --> pdb=" O ALA J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 92 Processing helix chain 'J' and resid 94 through 96 No H-bonds generated for 'chain 'J' and resid 94 through 96' Processing helix chain 'J' and resid 115 through 123 Processing helix chain 'J' and resid 184 through 189 Processing helix chain 'J' and resid 209 through 217 Processing helix chain 'J' and resid 224 through 227 No H-bonds generated for 'chain 'J' and resid 224 through 227' Processing helix chain 'J' and resid 230 through 235 Processing helix chain 'J' and resid 282 through 291 removed outlier: 3.996A pdb=" N ARG J 286 " --> pdb=" O TRP J 282 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TRP J 290 " --> pdb=" O ARG J 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 58 through 60 No H-bonds generated for 'chain 'L' and resid 58 through 60' Processing helix chain 'L' and resid 91 through 118 Processing helix chain 'L' and resid 123 through 133 Processing helix chain 'L' and resid 135 through 140 Processing helix chain 'L' and resid 146 through 157 removed outlier: 3.770A pdb=" N SER L 157 " --> pdb=" O LYS L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 162 through 164 No H-bonds generated for 'chain 'L' and resid 162 through 164' Processing helix chain 'L' and resid 169 through 182 removed outlier: 4.091A pdb=" N GLU L 173 " --> pdb=" O GLU L 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 203 through 216 Processing helix chain 'L' and resid 243 through 263 removed outlier: 3.842A pdb=" N SER L 248 " --> pdb=" O THR L 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 60 No H-bonds generated for 'chain 'M' and resid 58 through 60' Processing helix chain 'M' and resid 91 through 118 Processing helix chain 'M' and resid 123 through 133 Processing helix chain 'M' and resid 135 through 140 Processing helix chain 'M' and resid 146 through 157 removed outlier: 3.769A pdb=" N SER M 157 " --> pdb=" O LYS M 153 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 164 No H-bonds generated for 'chain 'M' and resid 162 through 164' Processing helix chain 'M' and resid 169 through 182 removed outlier: 4.092A pdb=" N GLU M 173 " --> pdb=" O GLU M 169 " (cutoff:3.500A) Processing helix chain 'M' and resid 203 through 216 Processing helix chain 'M' and resid 243 through 263 removed outlier: 3.842A pdb=" N SER M 248 " --> pdb=" O THR M 244 " (cutoff:3.500A) Processing helix chain 'S' and resid 54 through 61 Processing helix chain 'S' and resid 138 through 145 Processing helix chain 'S' and resid 166 through 178 Processing helix chain 'S' and resid 196 through 216 Processing helix chain 'S' and resid 229 through 242 Processing helix chain 'T' and resid 54 through 61 Processing helix chain 'T' and resid 138 through 145 Processing helix chain 'T' and resid 166 through 178 Processing helix chain 'T' and resid 196 through 216 Processing helix chain 'T' and resid 229 through 242 Processing helix chain 'd' and resid 4 through 15 Processing helix chain 'e' and resid 4 through 15 Processing sheet with id= A, first strand: chain 'A' and resid 149 through 152 removed outlier: 6.665A pdb=" N GLU A 90 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N LEU A 47 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE A 92 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL A 119 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL A 93 " --> pdb=" O VAL A 119 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ARG A 121 " --> pdb=" O VAL A 93 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N CYS A 95 " --> pdb=" O ARG A 121 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE A 123 " --> pdb=" O CYS A 95 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 155 through 157 Processing sheet with id= C, first strand: chain 'A' and resid 288 through 292 Processing sheet with id= D, first strand: chain 'A' and resid 239 through 241 Processing sheet with id= E, first strand: chain 'A' and resid 335 through 337 removed outlier: 6.216A pdb=" N VAL A 360 " --> pdb=" O TYR A 343 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLY A 345 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU A 362 " --> pdb=" O GLY A 345 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 407 through 409 removed outlier: 5.721A pdb=" N VAL A 390 " --> pdb=" O ILE A 408 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N PHE A 373 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE A 355 " --> pdb=" O ILE A 374 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'A' and resid 411 through 413 removed outlier: 6.751A pdb=" N SER A 429 " --> pdb=" O LEU A 412 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER A 447 " --> pdb=" O VAL A 430 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 149 through 152 removed outlier: 6.665A pdb=" N GLU B 90 " --> pdb=" O ALA B 45 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N LEU B 47 " --> pdb=" O GLU B 90 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N PHE B 92 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N VAL B 119 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N VAL B 93 " --> pdb=" O VAL B 119 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ARG B 121 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N CYS B 95 " --> pdb=" O ARG B 121 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ILE B 123 " --> pdb=" O CYS B 95 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 155 through 157 Processing sheet with id= J, first strand: chain 'B' and resid 288 through 292 Processing sheet with id= K, first strand: chain 'B' and resid 239 through 241 Processing sheet with id= L, first strand: chain 'B' and resid 335 through 337 removed outlier: 6.216A pdb=" N VAL B 360 " --> pdb=" O TYR B 343 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLY B 345 " --> pdb=" O VAL B 360 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N LEU B 362 " --> pdb=" O GLY B 345 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 407 through 409 removed outlier: 5.721A pdb=" N VAL B 390 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE B 373 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE B 355 " --> pdb=" O ILE B 374 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'B' and resid 411 through 413 removed outlier: 6.752A pdb=" N SER B 429 " --> pdb=" O LEU B 412 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N SER B 447 " --> pdb=" O VAL B 430 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.755A pdb=" N HIS C 188 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N THR C 167 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ILE C 190 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 231 through 234 removed outlier: 7.607A pdb=" N ILE C 234 " --> pdb=" O PRO C 264 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ILE C 266 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU C 323 " --> pdb=" O VAL C 267 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 245 through 248 Processing sheet with id= R, first strand: chain 'D' and resid 164 through 168 removed outlier: 6.662A pdb=" N HIS D 188 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N THR D 167 " --> pdb=" O HIS D 188 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE D 190 " --> pdb=" O THR D 167 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N THR D 215 " --> pdb=" O VAL D 191 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'D' and resid 232 through 234 removed outlier: 7.276A pdb=" N LEU D 323 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 245 through 248 Processing sheet with id= U, first strand: chain 'E' and resid 332 through 336 removed outlier: 6.638A pdb=" N ARG E 357 " --> pdb=" O ILE E 333 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N VAL E 335 " --> pdb=" O ARG E 357 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N VAL E 359 " --> pdb=" O VAL E 335 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL E 360 " --> pdb=" O PRO E 382 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N SER E 384 " --> pdb=" O VAL E 360 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N ASP E 362 " --> pdb=" O SER E 384 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N LEU E 386 " --> pdb=" O ASP E 362 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'E' and resid 400 through 404 removed outlier: 7.876A pdb=" N LEU E 403 " --> pdb=" O PRO E 433 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LEU E 435 " --> pdb=" O LEU E 403 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LEU E 499 " --> pdb=" O VAL E 436 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 332 through 336 removed outlier: 6.539A pdb=" N ARG F 357 " --> pdb=" O ILE F 333 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N VAL F 335 " --> pdb=" O ARG F 357 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL F 359 " --> pdb=" O VAL F 335 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL F 360 " --> pdb=" O PRO F 382 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N SER F 384 " --> pdb=" O VAL F 360 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N ASP F 362 " --> pdb=" O SER F 384 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU F 386 " --> pdb=" O ASP F 362 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'F' and resid 401 through 404 removed outlier: 6.144A pdb=" N LEU F 499 " --> pdb=" O VAL F 436 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 289 through 291 removed outlier: 3.587A pdb=" N LEU G 283 " --> pdb=" O PHE G 226 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL G 229 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU G 192 " --> pdb=" O THR G 124 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU G 126 " --> pdb=" O LEU G 192 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 206 through 208 removed outlier: 3.683A pdb=" N ASN G 208 " --> pdb=" O ASP G 274 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'H' and resid 289 through 291 removed outlier: 3.588A pdb=" N LEU H 283 " --> pdb=" O PHE H 226 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL H 229 " --> pdb=" O VAL H 195 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LEU H 192 " --> pdb=" O THR H 124 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU H 126 " --> pdb=" O LEU H 192 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 206 through 208 removed outlier: 3.684A pdb=" N ASN H 208 " --> pdb=" O ASP H 274 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'I' and resid 75 through 78 removed outlier: 6.943A pdb=" N VAL I 51 " --> pdb=" O VAL I 76 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N ILE I 78 " --> pdb=" O VAL I 51 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N VAL I 53 " --> pdb=" O ILE I 78 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ILE I 52 " --> pdb=" O PHE I 3 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA I 5 " --> pdb=" O ILE I 52 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL I 54 " --> pdb=" O ALA I 5 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL I 7 " --> pdb=" O VAL I 54 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASP I 100 " --> pdb=" O GLN I 4 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL I 6 " --> pdb=" O ASP I 100 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU I 102 " --> pdb=" O VAL I 6 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'I' and resid 193 through 196 removed outlier: 5.730A pdb=" N ASP I 161 " --> pdb=" O LEU I 167 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LEU I 167 " --> pdb=" O ASP I 161 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'J' and resid 75 through 78 removed outlier: 6.944A pdb=" N VAL J 51 " --> pdb=" O VAL J 76 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N ILE J 78 " --> pdb=" O VAL J 51 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N VAL J 53 " --> pdb=" O ILE J 78 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ILE J 52 " --> pdb=" O PHE J 3 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N ALA J 5 " --> pdb=" O ILE J 52 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N VAL J 54 " --> pdb=" O ALA J 5 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL J 7 " --> pdb=" O VAL J 54 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ASP J 100 " --> pdb=" O GLN J 4 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL J 6 " --> pdb=" O ASP J 100 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N LEU J 102 " --> pdb=" O VAL J 6 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'J' and resid 193 through 196 removed outlier: 5.730A pdb=" N ASP J 161 " --> pdb=" O LEU J 167 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU J 167 " --> pdb=" O ASP J 161 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'L' and resid 41 through 46 removed outlier: 3.867A pdb=" N ILE L 41 " --> pdb=" O LEU L 35 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N SER L 34 " --> pdb=" O VAL L 23 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL L 23 " --> pdb=" O SER L 34 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASP L 83 " --> pdb=" O ILE L 73 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N VAL L 75 " --> pdb=" O TYR L 81 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR L 81 " --> pdb=" O VAL L 75 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'L' and resid 224 through 227 Processing sheet with id= AI, first strand: chain 'M' and resid 41 through 46 removed outlier: 3.867A pdb=" N ILE M 41 " --> pdb=" O LEU M 35 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N SER M 34 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N VAL M 23 " --> pdb=" O SER M 34 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASP M 83 " --> pdb=" O ILE M 73 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL M 75 " --> pdb=" O TYR M 81 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR M 81 " --> pdb=" O VAL M 75 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 224 through 227 Processing sheet with id= AK, first strand: chain 'S' and resid 42 through 46 removed outlier: 4.656A pdb=" N CYS S 135 " --> pdb=" O THR S 46 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL S 127 " --> pdb=" O ILE S 88 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE S 88 " --> pdb=" O VAL S 127 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N HIS S 129 " --> pdb=" O ALA S 86 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ALA S 86 " --> pdb=" O HIS S 129 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N SER S 131 " --> pdb=" O ALA S 84 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N ALA S 84 " --> pdb=" O SER S 131 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL S 133 " --> pdb=" O GLY S 82 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY S 82 " --> pdb=" O VAL S 133 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'S' and resid 155 through 159 Processing sheet with id= AM, first strand: chain 'S' and resid 256 through 258 Processing sheet with id= AN, first strand: chain 'S' and resid 293 through 295 removed outlier: 3.600A pdb=" N SER S 316 " --> pdb=" O ILE S 294 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'S' and resid 300 through 302 Processing sheet with id= AP, first strand: chain 'S' and resid 461 through 465 removed outlier: 4.143A pdb=" N GLU S 370 " --> pdb=" O VAL S 463 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N ILE S 465 " --> pdb=" O PHE S 368 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N PHE S 368 " --> pdb=" O ILE S 465 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR S 369 " --> pdb=" O LEU S 429 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA S 419 " --> pdb=" O LYS S 426 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL S 428 " --> pdb=" O VAL S 417 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N VAL S 417 " --> pdb=" O VAL S 428 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'S' and resid 440 through 446 removed outlier: 5.654A pdb=" N ARG S 445 " --> pdb=" O LEU S 453 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU S 453 " --> pdb=" O ARG S 445 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'T' and resid 42 through 46 removed outlier: 4.655A pdb=" N CYS T 135 " --> pdb=" O THR T 46 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N VAL T 127 " --> pdb=" O ILE T 88 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N ILE T 88 " --> pdb=" O VAL T 127 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N HIS T 129 " --> pdb=" O ALA T 86 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ALA T 86 " --> pdb=" O HIS T 129 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER T 131 " --> pdb=" O ALA T 84 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N ALA T 84 " --> pdb=" O SER T 131 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N VAL T 133 " --> pdb=" O GLY T 82 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N GLY T 82 " --> pdb=" O VAL T 133 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'T' and resid 155 through 159 Processing sheet with id= AT, first strand: chain 'T' and resid 256 through 258 Processing sheet with id= AU, first strand: chain 'T' and resid 293 through 295 removed outlier: 3.599A pdb=" N SER T 316 " --> pdb=" O ILE T 294 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'T' and resid 300 through 302 Processing sheet with id= AW, first strand: chain 'T' and resid 461 through 465 removed outlier: 4.143A pdb=" N GLU T 370 " --> pdb=" O VAL T 463 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ILE T 465 " --> pdb=" O PHE T 368 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N PHE T 368 " --> pdb=" O ILE T 465 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N THR T 369 " --> pdb=" O LEU T 429 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA T 419 " --> pdb=" O LYS T 426 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL T 428 " --> pdb=" O VAL T 417 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N VAL T 417 " --> pdb=" O VAL T 428 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'T' and resid 440 through 446 removed outlier: 5.653A pdb=" N ARG T 445 " --> pdb=" O LEU T 453 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N LEU T 453 " --> pdb=" O ARG T 445 " (cutoff:3.500A) 1410 hydrogen bonds defined for protein. 4032 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: 12.88 Time building geometry restraints manager: 14.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5769 1.31 - 1.44: 8466 1.44 - 1.56: 19758 1.56 - 1.69: 1 1.69 - 1.82: 200 Bond restraints: 34194 Sorted by residual: bond pdb=" C16AC7B C 401 " pdb=" N08AC7B C 401 " ideal model delta sigma weight residual 1.341 1.464 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" C16BC7B C 401 " pdb=" N08BC7B C 401 " ideal model delta sigma weight residual 1.341 1.463 -0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" C15AC7B C 401 " pdb=" N07AC7B C 401 " ideal model delta sigma weight residual 1.341 1.454 -0.113 2.00e-02 2.50e+03 3.19e+01 bond pdb=" C15BC7B C 401 " pdb=" N07BC7B C 401 " ideal model delta sigma weight residual 1.341 1.453 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" CD2 TRP M 135 " pdb=" CE2 TRP M 135 " ideal model delta sigma weight residual 1.409 1.483 -0.074 1.70e-02 3.46e+03 1.91e+01 ... (remaining 34189 not shown) Histogram of bond angle deviations from ideal: 98.36 - 105.49: 567 105.49 - 112.62: 18215 112.62 - 119.75: 10495 119.75 - 126.88: 17100 126.88 - 134.01: 300 Bond angle restraints: 46677 Sorted by residual: angle pdb=" CD2 TRP L 135 " pdb=" CE3 TRP L 135 " pdb=" CZ3 TRP L 135 " ideal model delta sigma weight residual 118.60 129.48 -10.88 1.30e+00 5.92e-01 7.01e+01 angle pdb=" CD2 TRP M 135 " pdb=" CE3 TRP M 135 " pdb=" CZ3 TRP M 135 " ideal model delta sigma weight residual 118.60 129.41 -10.81 1.30e+00 5.92e-01 6.92e+01 angle pdb=" CE2 TRP M 135 " pdb=" CD2 TRP M 135 " pdb=" CE3 TRP M 135 " ideal model delta sigma weight residual 118.80 124.83 -6.03 1.00e+00 1.00e+00 3.63e+01 angle pdb=" CE2 TRP L 135 " pdb=" CD2 TRP L 135 " pdb=" CE3 TRP L 135 " ideal model delta sigma weight residual 118.80 124.76 -5.96 1.00e+00 1.00e+00 3.56e+01 angle pdb=" N ILE F 388 " pdb=" CA ILE F 388 " pdb=" C ILE F 388 " ideal model delta sigma weight residual 108.88 119.48 -10.60 2.16e+00 2.14e-01 2.41e+01 ... (remaining 46672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.83: 20006 29.83 - 59.66: 336 59.66 - 89.49: 29 89.49 - 119.32: 12 119.32 - 149.15: 2 Dihedral angle restraints: 20385 sinusoidal: 5946 harmonic: 14439 Sorted by residual: dihedral pdb=" CA LYS S 421 " pdb=" C LYS S 421 " pdb=" N ALA S 422 " pdb=" CA ALA S 422 " ideal model delta harmonic sigma weight residual 180.00 151.71 28.29 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA LYS T 421 " pdb=" C LYS T 421 " pdb=" N ALA T 422 " pdb=" CA ALA T 422 " ideal model delta harmonic sigma weight residual 180.00 151.73 28.27 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA LYS E 311 " pdb=" C LYS E 311 " pdb=" N ILE E 312 " pdb=" CA ILE E 312 " ideal model delta harmonic sigma weight residual 180.00 156.49 23.51 0 5.00e+00 4.00e-02 2.21e+01 ... (remaining 20382 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.020: 5694 1.020 - 2.040: 0 2.040 - 3.059: 0 3.059 - 4.079: 0 4.079 - 5.099: 4 Chirality restraints: 5698 Sorted by residual: chirality pdb=" C09BC7B C 401 " pdb=" C13BC7B C 401 " pdb=" C14BC7B C 401 " pdb=" N07BC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.63 5.10 2.00e-01 2.50e+01 6.50e+02 chirality pdb=" C09AC7B C 401 " pdb=" C13AC7B C 401 " pdb=" C14AC7B C 401 " pdb=" N07AC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.61 5.08 2.00e-01 2.50e+01 6.45e+02 chirality pdb=" C10BC7B C 401 " pdb=" C11BC7B C 401 " pdb=" C12BC7B C 401 " pdb=" N08BC7B C 401 " both_signs ideal model delta sigma weight residual False 2.47 -2.44 4.90 2.00e-01 2.50e+01 6.01e+02 ... (remaining 5695 not shown) Planarity restraints: 6130 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 395 " -0.053 5.00e-02 4.00e+02 8.03e-02 1.03e+01 pdb=" N PRO F 396 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO F 396 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 396 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU E 395 " 0.053 5.00e-02 4.00e+02 7.97e-02 1.02e+01 pdb=" N PRO E 396 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO E 396 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO E 396 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS S 421 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.25e+00 pdb=" C LYS S 421 " -0.043 2.00e-02 2.50e+03 pdb=" O LYS S 421 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA S 422 " 0.014 2.00e-02 2.50e+03 ... (remaining 6127 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 9856 2.81 - 3.33: 28657 3.33 - 3.85: 56037 3.85 - 4.38: 59971 4.38 - 4.90: 106049 Nonbonded interactions: 260570 Sorted by model distance: nonbonded pdb=" OG SER A 411 " pdb=" OG SER A 429 " model vdw 2.285 2.440 nonbonded pdb=" OG SER B 411 " pdb=" OG SER B 429 " model vdw 2.286 2.440 nonbonded pdb=" O GLU H 202 " pdb=" OG SER H 297 " model vdw 2.289 2.440 nonbonded pdb=" O GLU G 202 " pdb=" OG SER G 297 " model vdw 2.290 2.440 nonbonded pdb=" OG SER B 130 " pdb=" O GLN B 267 " model vdw 2.302 2.440 ... (remaining 260565 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 8 through 351) selection = (chain 'D' and (resid 8 through 98 or resid 126 through 351)) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 166 through 521 or (resid 522 and (name N or name CA or na \ me C or name O )))) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'L' selection = chain 'M' } ncs_group { reference = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'd' selection = chain 'e' } 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=0.50 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: 7.170 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: 0.030 Extract box with map and model: 27.670 Check model and map are aligned: 0.560 Set scattering table: 0.330 Process input model: 92.820 Find NCS groups from input model: 2.390 Set up NCS constraints: 0.320 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6416 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 : 0.004 0.123 34194 Z= 0.243 Angle : 0.714 17.013 46677 Z= 0.387 Chirality : 0.142 5.099 5698 Planarity : 0.006 0.080 6130 Dihedral : 12.344 149.152 10981 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.34 % Allowed : 4.86 % Favored : 94.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: -4.06 (0.09), residues: 4881 helix: -2.63 (0.08), residues: 1898 sheet: -2.54 (0.17), residues: 746 loop : -2.70 (0.11), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 272 HIS 0.003 0.001 HIS F 470 PHE 0.033 0.001 PHE C 177 TYR 0.015 0.001 TYR B 395 ARG 0.003 0.000 ARG H 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1017 time to evaluate : 3.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 LEU cc_start: 0.7085 (tp) cc_final: 0.6807 (tp) REVERT: A 264 PHE cc_start: 0.6197 (m-80) cc_final: 0.5955 (m-80) REVERT: A 310 CYS cc_start: 0.7566 (t) cc_final: 0.6965 (t) REVERT: B 218 THR cc_start: 0.6990 (p) cc_final: 0.5930 (m) REVERT: B 224 PHE cc_start: 0.7173 (m-80) cc_final: 0.6839 (m-80) REVERT: B 277 LEU cc_start: 0.8107 (mt) cc_final: 0.7808 (mt) REVERT: C 58 MET cc_start: 0.6717 (mtt) cc_final: 0.6494 (mtt) REVERT: C 129 LEU cc_start: 0.7882 (pt) cc_final: 0.7580 (tt) REVERT: D 134 ILE cc_start: 0.8529 (mm) cc_final: 0.8201 (tp) REVERT: D 138 ASN cc_start: 0.8678 (m-40) cc_final: 0.8461 (m110) REVERT: D 202 GLU cc_start: 0.6633 (pm20) cc_final: 0.6263 (pm20) REVERT: D 206 ASN cc_start: 0.7580 (m-40) cc_final: 0.7283 (m-40) REVERT: D 251 THR cc_start: 0.8415 (t) cc_final: 0.8064 (m) REVERT: F 260 MET cc_start: 0.7488 (mmp) cc_final: 0.5465 (ptp) REVERT: F 300 LEU cc_start: 0.7705 (mt) cc_final: 0.7310 (mt) REVERT: H 121 ASP cc_start: 0.5679 (t70) cc_final: 0.5417 (t70) REVERT: H 232 SER cc_start: 0.6514 (m) cc_final: 0.6228 (p) REVERT: I 46 VAL cc_start: 0.8621 (OUTLIER) cc_final: 0.8381 (m) REVERT: I 78 ILE cc_start: 0.7953 (pt) cc_final: 0.7711 (mm) REVERT: I 131 LEU cc_start: 0.6940 (tp) cc_final: 0.6651 (tp) REVERT: J 210 TYR cc_start: 0.6309 (p90) cc_final: 0.4543 (t80) REVERT: M 36 LEU cc_start: 0.8054 (mt) cc_final: 0.7578 (mp) outliers start: 9 outliers final: 1 residues processed: 1020 average time/residue: 0.5048 time to fit residues: 810.6534 Evaluate side-chains 599 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 597 time to evaluate : 3.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain I residue 46 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 415 optimal weight: 20.0000 chunk 372 optimal weight: 20.0000 chunk 206 optimal weight: 4.9990 chunk 127 optimal weight: 8.9990 chunk 251 optimal weight: 9.9990 chunk 199 optimal weight: 5.9990 chunk 385 optimal weight: 10.0000 chunk 149 optimal weight: 0.9990 chunk 234 optimal weight: 2.9990 chunk 287 optimal weight: 6.9990 chunk 446 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 HIS A 255 GLN A 337 HIS A 376 ASN B 72 ASN B 337 HIS B 376 ASN C 128 GLN C 158 HIS C 230 ASN C 277 GLN ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 230 ASN D 277 GLN D 331 ASN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 ASN E 254 ASN E 274 HIS ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 213 GLN F 406 HIS F 475 ASN F 477 GLN G 156 GLN ** G 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 156 GLN ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 41 ASN I 115 HIS I 172 ASN ** L 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.6188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.109 34194 Z= 0.628 Angle : 0.903 20.278 46677 Z= 0.463 Chirality : 0.054 0.391 5698 Planarity : 0.006 0.076 6130 Dihedral : 6.293 170.493 5261 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 6.32 % Allowed : 16.82 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.11), residues: 4881 helix: -0.79 (0.11), residues: 1921 sheet: -2.03 (0.18), residues: 695 loop : -2.32 (0.12), residues: 2265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 97 HIS 0.032 0.002 HIS B 192 PHE 0.037 0.003 PHE D 177 TYR 0.038 0.003 TYR B 266 ARG 0.012 0.001 ARG D 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 477 time to evaluate : 3.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ILE cc_start: 0.8468 (pt) cc_final: 0.8072 (pt) REVERT: A 289 MET cc_start: 0.8851 (ttp) cc_final: 0.8539 (ttp) REVERT: B 145 ARG cc_start: 0.7410 (mmm160) cc_final: 0.7164 (mmt-90) REVERT: B 303 LEU cc_start: 0.5315 (OUTLIER) cc_final: 0.5054 (pp) REVERT: C 128 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7375 (pm20) REVERT: C 143 GLU cc_start: 0.7741 (tp30) cc_final: 0.7374 (tp30) REVERT: D 93 TYR cc_start: 0.5385 (t80) cc_final: 0.4684 (t80) REVERT: D 197 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.7871 (p90) REVERT: D 202 GLU cc_start: 0.7447 (pm20) cc_final: 0.7244 (mp0) REVERT: E 309 GLN cc_start: 0.7848 (tp-100) cc_final: 0.7632 (tp-100) REVERT: F 282 LYS cc_start: 0.8666 (ttpt) cc_final: 0.8439 (tmtt) REVERT: G 186 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8961 (mt) REVERT: G 188 GLU cc_start: 0.8556 (pt0) cc_final: 0.8337 (pt0) REVERT: G 202 GLU cc_start: 0.7816 (tt0) cc_final: 0.7566 (tt0) REVERT: G 213 ASN cc_start: 0.9042 (t0) cc_final: 0.8740 (t0) REVERT: H 72 PHE cc_start: 0.8566 (t80) cc_final: 0.8349 (t80) REVERT: H 75 PHE cc_start: 0.9085 (t80) cc_final: 0.7322 (m-80) REVERT: H 130 TYR cc_start: 0.8303 (t80) cc_final: 0.8088 (t80) REVERT: H 290 VAL cc_start: 0.8816 (t) cc_final: 0.8418 (t) REVERT: J 125 ASP cc_start: 0.8405 (t70) cc_final: 0.7894 (t0) REVERT: M 36 LEU cc_start: 0.8505 (mt) cc_final: 0.8145 (mp) REVERT: M 37 GLU cc_start: 0.8415 (pt0) cc_final: 0.7891 (pm20) outliers start: 169 outliers final: 95 residues processed: 615 average time/residue: 0.4609 time to fit residues: 453.3427 Evaluate side-chains 465 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 366 time to evaluate : 4.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 396 LEU Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 128 GLN Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 238 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain D residue 340 MET Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 359 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 437 CYS Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 449 THR Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 183 VAL Chi-restraints excluded: chain G residue 186 ILE Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 236 VAL Chi-restraints excluded: chain G residue 282 THR Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 195 VAL Chi-restraints excluded: chain H residue 291 LEU Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 300 LEU Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 207 LEU Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain J residue 214 PHE Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 35 LEU Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain S residue 450 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 248 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 chunk 371 optimal weight: 5.9990 chunk 304 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 447 optimal weight: 9.9990 chunk 483 optimal weight: 7.9990 chunk 398 optimal weight: 7.9990 chunk 443 optimal weight: 0.0570 chunk 152 optimal weight: 0.7980 chunk 359 optimal weight: 10.0000 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS C 128 GLN C 154 GLN ** C 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN D 132 ASN D 154 GLN E 234 GLN E 371 HIS ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 HIS ** G 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 196 HIS ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 9 GLN M 40 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 34194 Z= 0.165 Angle : 0.549 10.544 46677 Z= 0.279 Chirality : 0.044 0.231 5698 Planarity : 0.004 0.062 6130 Dihedral : 5.551 179.162 5259 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.44 % Allowed : 20.22 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: -1.49 (0.12), residues: 4881 helix: 0.40 (0.12), residues: 1914 sheet: -1.73 (0.19), residues: 666 loop : -1.97 (0.12), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 111 HIS 0.006 0.001 HIS C 158 PHE 0.021 0.001 PHE D 177 TYR 0.016 0.001 TYR A 128 ARG 0.008 0.001 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 422 time to evaluate : 4.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 86 THR cc_start: 0.8316 (OUTLIER) cc_final: 0.8052 (m) REVERT: B 145 ARG cc_start: 0.7206 (mmm160) cc_final: 0.6971 (mmm160) REVERT: C 143 GLU cc_start: 0.7656 (tp30) cc_final: 0.7344 (tp30) REVERT: C 314 ASP cc_start: 0.7816 (m-30) cc_final: 0.7598 (m-30) REVERT: D 93 TYR cc_start: 0.5128 (t80) cc_final: 0.4665 (t80) REVERT: D 197 PHE cc_start: 0.8320 (OUTLIER) cc_final: 0.7599 (p90) REVERT: F 333 ILE cc_start: 0.8942 (OUTLIER) cc_final: 0.8666 (mt) REVERT: F 415 MET cc_start: 0.8035 (tpp) cc_final: 0.7601 (tpt) REVERT: G 213 ASN cc_start: 0.8935 (t0) cc_final: 0.8564 (t0) REVERT: H 72 PHE cc_start: 0.8530 (t80) cc_final: 0.8013 (t80) REVERT: H 75 PHE cc_start: 0.9063 (t80) cc_final: 0.7311 (m-80) REVERT: H 130 TYR cc_start: 0.8412 (t80) cc_final: 0.8152 (t80) REVERT: J 125 ASP cc_start: 0.8243 (t70) cc_final: 0.7643 (t0) REVERT: J 170 MET cc_start: 0.8457 (ttp) cc_final: 0.8250 (ttp) REVERT: J 210 TYR cc_start: 0.8003 (p90) cc_final: 0.5340 (t80) REVERT: M 36 LEU cc_start: 0.8456 (mt) cc_final: 0.8182 (mp) outliers start: 92 outliers final: 51 residues processed: 489 average time/residue: 0.4566 time to fit residues: 361.1531 Evaluate side-chains 419 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 365 time to evaluate : 4.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 388 ASN Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 251 ILE Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 360 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 498 ASP Chi-restraints excluded: chain E residue 504 LEU Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 386 LEU Chi-restraints excluded: chain F residue 459 ASP Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 288 LEU Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 103 ARG Chi-restraints excluded: chain H residue 109 ASN Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 214 PHE Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 33 VAL Chi-restraints excluded: chain S residue 450 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 442 optimal weight: 30.0000 chunk 336 optimal weight: 9.9990 chunk 232 optimal weight: 6.9990 chunk 49 optimal weight: 50.0000 chunk 213 optimal weight: 0.0470 chunk 300 optimal weight: 0.6980 chunk 449 optimal weight: 40.0000 chunk 475 optimal weight: 30.0000 chunk 234 optimal weight: 10.0000 chunk 425 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 overall best weight: 3.5484 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 ASN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 160 ASN B 255 GLN B 337 HIS C 150 ASN C 154 GLN C 277 GLN D 138 ASN D 150 ASN D 261 HIS ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 GLN ** G 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.8159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 34194 Z= 0.508 Angle : 0.734 11.886 46677 Z= 0.378 Chirality : 0.049 0.245 5698 Planarity : 0.005 0.064 6130 Dihedral : 6.065 179.344 5259 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.31 % Favored : 93.63 % Rotamer: Outliers : 5.87 % Allowed : 20.34 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: -1.16 (0.12), residues: 4881 helix: 0.74 (0.12), residues: 1911 sheet: -1.76 (0.18), residues: 735 loop : -1.76 (0.13), residues: 2235 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP S 456 HIS 0.008 0.002 HIS F 274 PHE 0.029 0.002 PHE D 177 TYR 0.032 0.002 TYR D 315 ARG 0.009 0.001 ARG L 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 523 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 366 time to evaluate : 4.243 Fit side-chains revert: symmetry clash REVERT: A 128 TYR cc_start: 0.8045 (OUTLIER) cc_final: 0.4739 (p90) REVERT: B 86 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8763 (m) REVERT: B 459 ASP cc_start: 0.5377 (OUTLIER) cc_final: 0.5092 (p0) REVERT: C 91 GLU cc_start: 0.8152 (pp20) cc_final: 0.7716 (tp30) REVERT: D 93 TYR cc_start: 0.5774 (t80) cc_final: 0.5001 (t80) REVERT: D 197 PHE cc_start: 0.8680 (OUTLIER) cc_final: 0.7974 (p90) REVERT: F 260 MET cc_start: 0.8930 (mmp) cc_final: 0.8723 (mmp) REVERT: F 415 MET cc_start: 0.7961 (tpp) cc_final: 0.7689 (tpt) REVERT: G 101 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8754 (tp) REVERT: G 126 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9065 (tt) REVERT: G 213 ASN cc_start: 0.9156 (t0) cc_final: 0.8886 (t0) REVERT: H 93 MET cc_start: 0.8812 (mmm) cc_final: 0.8498 (mmt) REVERT: I 50 GLU cc_start: 0.8351 (tp30) cc_final: 0.7977 (tm-30) REVERT: I 210 TYR cc_start: 0.8259 (p90) cc_final: 0.6175 (t80) REVERT: J 97 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7831 (pp) REVERT: J 125 ASP cc_start: 0.8776 (t70) cc_final: 0.8524 (t0) REVERT: L 3 LEU cc_start: 0.6954 (tt) cc_final: 0.6544 (tp) REVERT: L 76 ASP cc_start: 0.8459 (t0) cc_final: 0.8134 (t0) REVERT: L 86 LYS cc_start: 0.8861 (tptm) cc_final: 0.8627 (mmmm) REVERT: M 54 ARG cc_start: 0.8385 (tpt90) cc_final: 0.8111 (tpt90) REVERT: S 446 ARG cc_start: 0.8508 (ttm170) cc_final: 0.8285 (ttm-80) outliers start: 157 outliers final: 106 residues processed: 495 average time/residue: 0.4712 time to fit residues: 378.9716 Evaluate side-chains 435 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 322 time to evaluate : 4.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 302 ASN Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 253 SER Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 394 THR Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 248 VAL Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 253 THR Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 220 SER Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 394 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 497 VAL Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 434 VAL Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain F residue 459 ASP Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 101 LEU Chi-restraints excluded: chain G residue 115 CYS Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 160 VAL Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 160 VAL Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 214 PHE Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain S residue 450 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 396 optimal weight: 20.0000 chunk 269 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 354 optimal weight: 4.9990 chunk 196 optimal weight: 0.7980 chunk 405 optimal weight: 4.9990 chunk 328 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 chunk 242 optimal weight: 4.9990 chunk 426 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 ASN B 72 ASN C 150 ASN C 277 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 325 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 4 GLN J 115 HIS ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.8205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34194 Z= 0.188 Angle : 0.541 13.063 46677 Z= 0.275 Chirality : 0.044 0.163 5698 Planarity : 0.004 0.062 6130 Dihedral : 5.560 179.044 5259 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.00 % Favored : 95.96 % Rotamer: Outliers : 3.66 % Allowed : 22.17 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: -0.65 (0.12), residues: 4881 helix: 1.25 (0.12), residues: 1957 sheet: -1.54 (0.18), residues: 715 loop : -1.60 (0.13), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 111 HIS 0.003 0.001 HIS A 337 PHE 0.018 0.001 PHE D 177 TYR 0.020 0.001 TYR G 86 ARG 0.007 0.000 ARG E 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 376 time to evaluate : 4.040 Fit side-chains revert: symmetry clash REVERT: A 459 ASP cc_start: 0.6251 (OUTLIER) cc_final: 0.6023 (p0) REVERT: B 65 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7852 (ttm170) REVERT: B 86 THR cc_start: 0.8914 (OUTLIER) cc_final: 0.8690 (m) REVERT: C 91 GLU cc_start: 0.8029 (pp20) cc_final: 0.7660 (tp30) REVERT: D 58 MET cc_start: 0.8641 (mmm) cc_final: 0.8125 (mtt) REVERT: D 93 TYR cc_start: 0.5947 (t80) cc_final: 0.5283 (t80) REVERT: D 163 GLU cc_start: 0.6916 (tt0) cc_final: 0.6580 (tt0) REVERT: D 197 PHE cc_start: 0.8515 (OUTLIER) cc_final: 0.7713 (p90) REVERT: D 319 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8157 (pm20) REVERT: E 324 TYR cc_start: 0.7493 (t80) cc_final: 0.7184 (t80) REVERT: F 415 MET cc_start: 0.7930 (tpp) cc_final: 0.7532 (tpt) REVERT: G 213 ASN cc_start: 0.9040 (t0) cc_final: 0.8676 (t0) REVERT: I 209 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8471 (tptt) REVERT: I 210 TYR cc_start: 0.8038 (p90) cc_final: 0.5940 (t80) REVERT: J 210 TYR cc_start: 0.8259 (p90) cc_final: 0.5692 (t80) REVERT: L 3 LEU cc_start: 0.7023 (tt) cc_final: 0.6637 (tp) REVERT: L 76 ASP cc_start: 0.8418 (t0) cc_final: 0.8174 (t0) REVERT: L 86 LYS cc_start: 0.8825 (tptm) cc_final: 0.8596 (mmmm) outliers start: 98 outliers final: 67 residues processed: 454 average time/residue: 0.4625 time to fit residues: 338.8793 Evaluate side-chains 414 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 341 time to evaluate : 4.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 319 GLU Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain F residue 202 VAL Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain F residue 484 LEU Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 214 PHE Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain S residue 450 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 160 optimal weight: 5.9990 chunk 428 optimal weight: 30.0000 chunk 94 optimal weight: 5.9990 chunk 279 optimal weight: 0.0870 chunk 117 optimal weight: 8.9990 chunk 476 optimal weight: 50.0000 chunk 395 optimal weight: 8.9990 chunk 220 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 157 optimal weight: 0.9990 chunk 249 optimal weight: 1.9990 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 ASN H 243 GLN I 190 HIS ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.8488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 34194 Z= 0.284 Angle : 0.568 14.939 46677 Z= 0.287 Chirality : 0.045 0.162 5698 Planarity : 0.004 0.062 6130 Dihedral : 5.527 179.140 5259 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.29 % Favored : 94.67 % Rotamer: Outliers : 4.45 % Allowed : 22.73 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: -0.42 (0.12), residues: 4881 helix: 1.49 (0.12), residues: 1959 sheet: -1.44 (0.18), residues: 715 loop : -1.52 (0.13), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 111 HIS 0.004 0.001 HIS F 274 PHE 0.022 0.002 PHE D 177 TYR 0.020 0.001 TYR G 86 ARG 0.008 0.000 ARG M 54 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 357 time to evaluate : 3.907 Fit side-chains revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7811 (tt0) REVERT: A 251 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8569 (pt) REVERT: B 65 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.8045 (ttm170) REVERT: B 86 THR cc_start: 0.8972 (OUTLIER) cc_final: 0.8756 (m) REVERT: B 128 TYR cc_start: 0.7146 (OUTLIER) cc_final: 0.5422 (p90) REVERT: C 91 GLU cc_start: 0.8080 (pp20) cc_final: 0.7702 (tp30) REVERT: D 58 MET cc_start: 0.8605 (mmm) cc_final: 0.8356 (mtt) REVERT: D 93 TYR cc_start: 0.6121 (t80) cc_final: 0.5489 (t80) REVERT: D 197 PHE cc_start: 0.8573 (OUTLIER) cc_final: 0.7779 (p90) REVERT: E 495 GLU cc_start: 0.8664 (pm20) cc_final: 0.8377 (pm20) REVERT: F 235 GLN cc_start: 0.8966 (OUTLIER) cc_final: 0.8765 (mt0) REVERT: F 415 MET cc_start: 0.7973 (tpp) cc_final: 0.7599 (tpt) REVERT: G 213 ASN cc_start: 0.9114 (t0) cc_final: 0.8758 (t0) REVERT: H 130 TYR cc_start: 0.9032 (t80) cc_final: 0.8726 (t80) REVERT: I 50 GLU cc_start: 0.8314 (tp30) cc_final: 0.7984 (tm-30) REVERT: I 209 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8621 (tptt) REVERT: I 210 TYR cc_start: 0.8164 (p90) cc_final: 0.6102 (t80) REVERT: J 97 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8132 (pp) REVERT: L 3 LEU cc_start: 0.7120 (tt) cc_final: 0.6575 (tp) REVERT: L 76 ASP cc_start: 0.8449 (t0) cc_final: 0.8216 (t0) outliers start: 119 outliers final: 94 residues processed: 451 average time/residue: 0.4598 time to fit residues: 336.1528 Evaluate side-chains 441 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 339 time to evaluate : 4.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 72 ASN Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 54 VAL Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 214 PHE Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain S residue 450 HIS Chi-restraints excluded: chain T residue 456 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 458 optimal weight: 20.0000 chunk 53 optimal weight: 40.0000 chunk 271 optimal weight: 1.9990 chunk 347 optimal weight: 3.9990 chunk 269 optimal weight: 0.5980 chunk 400 optimal weight: 7.9990 chunk 265 optimal weight: 5.9990 chunk 474 optimal weight: 5.9990 chunk 296 optimal weight: 0.9980 chunk 289 optimal weight: 5.9990 chunk 218 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 376 ASN ** B 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 261 HIS ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.8719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 34194 Z= 0.245 Angle : 0.553 14.352 46677 Z= 0.279 Chirality : 0.044 0.157 5698 Planarity : 0.003 0.062 6130 Dihedral : 5.467 178.126 5259 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.47 % Favored : 95.49 % Rotamer: Outliers : 4.79 % Allowed : 22.32 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: -0.25 (0.12), residues: 4881 helix: 1.69 (0.12), residues: 1953 sheet: -1.48 (0.18), residues: 727 loop : -1.42 (0.13), residues: 2201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 111 HIS 0.003 0.001 HIS A 304 PHE 0.021 0.001 PHE D 177 TYR 0.025 0.001 TYR G 86 ARG 0.009 0.000 ARG M 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 349 time to evaluate : 4.189 Fit side-chains revert: symmetry clash REVERT: A 128 TYR cc_start: 0.7826 (OUTLIER) cc_final: 0.4488 (p90) REVERT: B 128 TYR cc_start: 0.7150 (OUTLIER) cc_final: 0.3957 (p90) REVERT: C 91 GLU cc_start: 0.8033 (pp20) cc_final: 0.7696 (tp30) REVERT: D 68 MET cc_start: 0.8604 (mmm) cc_final: 0.8402 (mtp) REVERT: D 93 TYR cc_start: 0.6392 (t80) cc_final: 0.5757 (t80) REVERT: D 197 PHE cc_start: 0.8558 (OUTLIER) cc_final: 0.7705 (p90) REVERT: E 495 GLU cc_start: 0.8641 (pm20) cc_final: 0.8407 (pm20) REVERT: F 235 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8761 (mt0) REVERT: F 415 MET cc_start: 0.7946 (tpp) cc_final: 0.7578 (tpt) REVERT: G 20 MET cc_start: 0.7280 (tpp) cc_final: 0.7015 (tpp) REVERT: G 213 ASN cc_start: 0.9112 (t0) cc_final: 0.8777 (t0) REVERT: H 103 ARG cc_start: 0.6827 (ttt180) cc_final: 0.6626 (ttt180) REVERT: H 130 TYR cc_start: 0.9020 (t80) cc_final: 0.8768 (t80) REVERT: I 50 GLU cc_start: 0.8324 (tp30) cc_final: 0.8014 (tm-30) REVERT: I 209 LYS cc_start: 0.8891 (OUTLIER) cc_final: 0.8620 (tptt) REVERT: I 210 TYR cc_start: 0.8216 (p90) cc_final: 0.6154 (t80) REVERT: J 8 MET cc_start: 0.8758 (mmm) cc_final: 0.8433 (mmm) REVERT: J 97 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8168 (pp) REVERT: L 3 LEU cc_start: 0.7125 (tt) cc_final: 0.6651 (tp) REVERT: L 76 ASP cc_start: 0.8459 (t0) cc_final: 0.8246 (t0) outliers start: 128 outliers final: 100 residues processed: 453 average time/residue: 0.4526 time to fit residues: 335.7671 Evaluate side-chains 440 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 334 time to evaluate : 3.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 97 HIS Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 284 ILE Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 457 LEU Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 126 LEU Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 169 CYS Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain I residue 263 ILE Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 214 PHE Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain S residue 450 HIS Chi-restraints excluded: chain T residue 456 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 293 optimal weight: 4.9990 chunk 189 optimal weight: 0.2980 chunk 283 optimal weight: 8.9990 chunk 142 optimal weight: 0.0970 chunk 93 optimal weight: 0.4980 chunk 91 optimal weight: 0.8980 chunk 301 optimal weight: 0.9990 chunk 323 optimal weight: 4.9990 chunk 234 optimal weight: 10.0000 chunk 44 optimal weight: 40.0000 chunk 372 optimal weight: 0.0770 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 HIS A 376 ASN ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 GLN E 275 ASN E 325 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 HIS H 214 GLN H 270 HIS ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.8707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 34194 Z= 0.139 Angle : 0.522 15.433 46677 Z= 0.261 Chirality : 0.043 0.155 5698 Planarity : 0.003 0.060 6130 Dihedral : 5.286 179.736 5259 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.53 % Favored : 95.43 % Rotamer: Outliers : 3.48 % Allowed : 23.55 % Favored : 72.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: 0.06 (0.13), residues: 4881 helix: 2.00 (0.12), residues: 1932 sheet: -1.31 (0.19), residues: 681 loop : -1.29 (0.13), residues: 2268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 111 HIS 0.004 0.001 HIS A 304 PHE 0.017 0.001 PHE D 177 TYR 0.019 0.001 TYR G 86 ARG 0.009 0.000 ARG S 452 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 375 time to evaluate : 3.832 Fit side-chains revert: symmetry clash REVERT: A 295 GLU cc_start: 0.7688 (mp0) cc_final: 0.7430 (mp0) REVERT: A 459 ASP cc_start: 0.6092 (OUTLIER) cc_final: 0.5892 (p0) REVERT: C 91 GLU cc_start: 0.8233 (pp20) cc_final: 0.7960 (pp20) REVERT: D 45 ILE cc_start: 0.8202 (mt) cc_final: 0.7916 (mt) REVERT: D 68 MET cc_start: 0.8589 (mmm) cc_final: 0.8267 (tpp) REVERT: D 93 TYR cc_start: 0.6321 (t80) cc_final: 0.5723 (t80) REVERT: D 166 MET cc_start: 0.8103 (ttm) cc_final: 0.7805 (ttt) REVERT: D 197 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7565 (p90) REVERT: E 495 GLU cc_start: 0.8617 (pm20) cc_final: 0.8340 (pm20) REVERT: F 415 MET cc_start: 0.7916 (tpp) cc_final: 0.7465 (tpt) REVERT: G 20 MET cc_start: 0.7244 (tpp) cc_final: 0.6933 (tpp) REVERT: G 213 ASN cc_start: 0.9081 (t0) cc_final: 0.8753 (t0) REVERT: I 50 GLU cc_start: 0.8301 (tp30) cc_final: 0.8004 (tm-30) REVERT: I 210 TYR cc_start: 0.8072 (p90) cc_final: 0.6075 (t80) REVERT: J 8 MET cc_start: 0.8823 (mmm) cc_final: 0.8549 (mmm) REVERT: J 97 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8152 (pp) REVERT: J 210 TYR cc_start: 0.8179 (p90) cc_final: 0.5769 (t80) REVERT: L 3 LEU cc_start: 0.7061 (tt) cc_final: 0.6717 (tp) REVERT: M 52 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6513 (ptt180) outliers start: 93 outliers final: 76 residues processed: 449 average time/residue: 0.4439 time to fit residues: 323.8562 Evaluate side-chains 426 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 346 time to evaluate : 3.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 188 SER Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 154 GLN Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 461 ASP Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 156 ASP Chi-restraints excluded: chain J residue 214 PHE Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 52 ARG Chi-restraints excluded: chain T residue 456 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 431 optimal weight: 50.0000 chunk 454 optimal weight: 4.9990 chunk 414 optimal weight: 5.9990 chunk 441 optimal weight: 40.0000 chunk 265 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 346 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 399 optimal weight: 20.0000 chunk 417 optimal weight: 0.6980 chunk 440 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN D 154 GLN E 234 GLN E 275 ASN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 245 ASN G 270 HIS ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.9217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.089 34194 Z= 0.500 Angle : 0.696 15.336 46677 Z= 0.351 Chirality : 0.048 0.228 5698 Planarity : 0.004 0.061 6130 Dihedral : 5.808 176.226 5259 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.74 % Favored : 93.22 % Rotamer: Outliers : 4.34 % Allowed : 23.07 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: -0.40 (0.12), residues: 4881 helix: 1.52 (0.12), residues: 1938 sheet: -1.53 (0.18), residues: 755 loop : -1.44 (0.13), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 111 HIS 0.006 0.001 HIS B 105 PHE 0.029 0.002 PHE D 177 TYR 0.024 0.002 TYR A 128 ARG 0.009 0.001 ARG S 452 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 318 time to evaluate : 4.258 Fit side-chains revert: symmetry clash REVERT: A 128 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.4487 (p90) REVERT: A 251 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8669 (pt) REVERT: B 86 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8827 (m) REVERT: B 128 TYR cc_start: 0.7636 (OUTLIER) cc_final: 0.3992 (p90) REVERT: C 91 GLU cc_start: 0.8377 (pp20) cc_final: 0.8071 (pp20) REVERT: D 68 MET cc_start: 0.8661 (mmm) cc_final: 0.8442 (tpp) REVERT: D 93 TYR cc_start: 0.6765 (t80) cc_final: 0.6179 (t80) REVERT: D 197 PHE cc_start: 0.8682 (OUTLIER) cc_final: 0.7977 (p90) REVERT: F 260 MET cc_start: 0.8803 (mmp) cc_final: 0.8563 (mmp) REVERT: G 213 ASN cc_start: 0.9113 (t0) cc_final: 0.8780 (t0) REVERT: H 103 ARG cc_start: 0.6912 (ttt180) cc_final: 0.6697 (ttt180) REVERT: I 50 GLU cc_start: 0.8385 (tp30) cc_final: 0.8109 (tm-30) REVERT: J 8 MET cc_start: 0.8858 (mmm) cc_final: 0.8512 (mmm) REVERT: J 41 ASN cc_start: 0.8082 (t0) cc_final: 0.7510 (t0) REVERT: L 3 LEU cc_start: 0.7473 (tt) cc_final: 0.7237 (tp) REVERT: L 42 GLU cc_start: 0.7623 (tp30) cc_final: 0.7352 (tp30) REVERT: L 126 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7880 (tt) outliers start: 116 outliers final: 96 residues processed: 416 average time/residue: 0.4438 time to fit residues: 301.4015 Evaluate side-chains 411 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 309 time to evaluate : 4.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 72 ASN Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 128 TYR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 307 SER Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain B residue 51 SER Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 128 TYR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 162 THR Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 304 GLU Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 193 VAL Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 53 ILE Chi-restraints excluded: chain H residue 71 LEU Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 156 ASP Chi-restraints excluded: chain J residue 193 ILE Chi-restraints excluded: chain J residue 214 PHE Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain L residue 152 PHE Chi-restraints excluded: chain M residue 22 ASN Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain M residue 37 GLU Chi-restraints excluded: chain S residue 450 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 290 optimal weight: 2.9990 chunk 467 optimal weight: 20.0000 chunk 285 optimal weight: 3.9990 chunk 221 optimal weight: 0.9980 chunk 324 optimal weight: 20.0000 chunk 490 optimal weight: 20.0000 chunk 451 optimal weight: 50.0000 chunk 390 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 301 optimal weight: 0.5980 chunk 239 optimal weight: 0.6980 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 40 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.9275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 34194 Z= 0.271 Angle : 0.591 15.979 46677 Z= 0.293 Chirality : 0.045 0.172 5698 Planarity : 0.004 0.060 6130 Dihedral : 5.619 179.967 5259 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.81 % Favored : 95.14 % Rotamer: Outliers : 3.55 % Allowed : 23.81 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: -0.12 (0.12), residues: 4881 helix: 1.79 (0.12), residues: 1937 sheet: -1.43 (0.18), residues: 749 loop : -1.30 (0.13), residues: 2195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 111 HIS 0.003 0.001 HIS G 128 PHE 0.021 0.001 PHE D 177 TYR 0.020 0.001 TYR B 78 ARG 0.009 0.000 ARG S 452 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9762 Ramachandran restraints generated. 4881 Oldfield, 0 Emsley, 4881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 331 time to evaluate : 4.638 Fit side-chains revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8136 (tt0) cc_final: 0.7910 (tt0) REVERT: B 181 MET cc_start: 0.8670 (ttm) cc_final: 0.8454 (ttm) REVERT: C 91 GLU cc_start: 0.8346 (pp20) cc_final: 0.8048 (pp20) REVERT: D 93 TYR cc_start: 0.7025 (t80) cc_final: 0.6547 (t80) REVERT: D 197 PHE cc_start: 0.8569 (OUTLIER) cc_final: 0.7790 (p90) REVERT: F 260 MET cc_start: 0.8760 (mmp) cc_final: 0.8515 (mmp) REVERT: G 213 ASN cc_start: 0.9077 (t0) cc_final: 0.8736 (t0) REVERT: H 103 ARG cc_start: 0.6905 (ttt180) cc_final: 0.6672 (ttt180) REVERT: I 50 GLU cc_start: 0.8354 (tp30) cc_final: 0.8081 (tm-30) REVERT: I 209 LYS cc_start: 0.8798 (OUTLIER) cc_final: 0.8563 (tptt) REVERT: I 210 TYR cc_start: 0.8248 (p90) cc_final: 0.6310 (t80) REVERT: J 8 MET cc_start: 0.8875 (mmm) cc_final: 0.8581 (mmm) REVERT: L 42 GLU cc_start: 0.7623 (tp30) cc_final: 0.7334 (tp30) REVERT: L 126 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7850 (tt) outliers start: 95 outliers final: 82 residues processed: 409 average time/residue: 0.4690 time to fit residues: 316.7592 Evaluate side-chains 400 residues out of total 4311 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 315 time to evaluate : 3.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 247 CYS Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 264 PHE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 432 THR Chi-restraints excluded: chain A residue 459 ASP Chi-restraints excluded: chain B residue 62 ASP Chi-restraints excluded: chain B residue 124 THR Chi-restraints excluded: chain B residue 138 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 212 VAL Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 264 PHE Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 282 ILE Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 322 THR Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 362 LEU Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 432 THR Chi-restraints excluded: chain C residue 32 GLU Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 219 ASP Chi-restraints excluded: chain C residue 271 MET Chi-restraints excluded: chain C residue 327 ASN Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 197 PHE Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 298 THR Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain E residue 332 VAL Chi-restraints excluded: chain E residue 388 ILE Chi-restraints excluded: chain E residue 434 VAL Chi-restraints excluded: chain E residue 444 CYS Chi-restraints excluded: chain E residue 499 LEU Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 516 LEU Chi-restraints excluded: chain F residue 253 VAL Chi-restraints excluded: chain F residue 257 LYS Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 313 VAL Chi-restraints excluded: chain F residue 333 ILE Chi-restraints excluded: chain F residue 358 VAL Chi-restraints excluded: chain F residue 381 VAL Chi-restraints excluded: chain F residue 481 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 273 VAL Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 176 THR Chi-restraints excluded: chain H residue 191 ASP Chi-restraints excluded: chain H residue 193 VAL Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 294 SER Chi-restraints excluded: chain H residue 305 LEU Chi-restraints excluded: chain I residue 93 ILE Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 158 ILE Chi-restraints excluded: chain I residue 180 LEU Chi-restraints excluded: chain I residue 181 VAL Chi-restraints excluded: chain I residue 209 LYS Chi-restraints excluded: chain J residue 52 ILE Chi-restraints excluded: chain J residue 86 THR Chi-restraints excluded: chain J residue 156 ASP Chi-restraints excluded: chain J residue 168 LEU Chi-restraints excluded: chain J residue 214 PHE Chi-restraints excluded: chain L residue 20 MET Chi-restraints excluded: chain L residue 22 ASN Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 126 LEU Chi-restraints excluded: chain M residue 25 SER Chi-restraints excluded: chain S residue 450 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 492 random chunks: chunk 310 optimal weight: 20.0000 chunk 415 optimal weight: 30.0000 chunk 119 optimal weight: 8.9990 chunk 359 optimal weight: 0.0020 chunk 57 optimal weight: 6.9990 chunk 108 optimal weight: 7.9990 chunk 390 optimal weight: 10.0000 chunk 163 optimal weight: 0.9980 chunk 401 optimal weight: 6.9990 chunk 49 optimal weight: 50.0000 chunk 72 optimal weight: 5.9990 overall best weight: 4.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN ** E 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 464 GLN ** L 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.109002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.078393 restraints weight = 124482.498| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.70 r_work: 0.3075 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3082 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3082 r_free = 0.3082 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3082 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.9675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.093 34194 Z= 0.521 Angle : 0.718 15.492 46677 Z= 0.361 Chirality : 0.049 0.224 5698 Planarity : 0.005 0.061 6130 Dihedral : 6.037 179.910 5259 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.33 % Favored : 92.62 % Rotamer: Outliers : 4.11 % Allowed : 23.44 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.04 % 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: -0.49 (0.12), residues: 4881 helix: 1.43 (0.12), residues: 1919 sheet: -1.53 (0.18), residues: 745 loop : -1.48 (0.13), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 111 HIS 0.006 0.001 HIS D 49 PHE 0.024 0.002 PHE D 177 TYR 0.029 0.002 TYR A 128 ARG 0.009 0.001 ARG S 452 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9301.85 seconds wall clock time: 166 minutes 39.64 seconds (9999.64 seconds total)