Starting phenix.real_space_refine on Wed Mar 20 22:59:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5s_14336/03_2024/7r5s_14336.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5s_14336/03_2024/7r5s_14336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5s_14336/03_2024/7r5s_14336.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5s_14336/03_2024/7r5s_14336.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5s_14336/03_2024/7r5s_14336.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r5s_14336/03_2024/7r5s_14336.pdb" } resolution = 2.83 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1895 atoms to isotropic. 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 P 82 5.49 5 S 139 5.16 5 C 16926 2.51 5 N 4596 2.21 5 O 5128 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H GLU 90": "OE1" <-> "OE2" Residue "H ASP 104": "OD1" <-> "OD2" Residue "H ASP 187": "OD1" <-> "OD2" Residue "H GLU 190": "OE1" <-> "OE2" Residue "H ASP 245": "OD1" <-> "OD2" Residue "I GLU 63": "OE1" <-> "OE2" Residue "I GLU 74": "OE1" <-> "OE2" Residue "I ASP 85": "OD1" <-> "OD2" Residue "I GLU 107": "OE1" <-> "OE2" Residue "I ASP 142": "OD1" <-> "OD2" Residue "I PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 179": "OE1" <-> "OE2" Residue "I TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 194": "OD1" <-> "OD2" Residue "I ASP 195": "OD1" <-> "OD2" Residue "I GLU 212": "OE1" <-> "OE2" Residue "I PHE 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 266": "OE1" <-> "OE2" Residue "I TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 331": "OD1" <-> "OD2" Residue "I ASP 381": "OD1" <-> "OD2" Residue "I GLU 409": "OE1" <-> "OE2" Residue "I PHE 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 639": "OE1" <-> "OE2" Residue "I ASP 664": "OD1" <-> "OD2" Residue "I GLU 666": "OE1" <-> "OE2" Residue "I TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 30": "OE1" <-> "OE2" Residue "K GLU 48": "OE1" <-> "OE2" Residue "K ASP 52": "OD1" <-> "OD2" Residue "K ASP 130": "OD1" <-> "OD2" Residue "K ASP 186": "OD1" <-> "OD2" Residue "K ASP 192": "OD1" <-> "OD2" Residue "K ASP 225": "OD1" <-> "OD2" Residue "K GLU 257": "OE1" <-> "OE2" Residue "L TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 176": "OE1" <-> "OE2" Residue "L ASP 231": "OD1" <-> "OD2" Residue "L PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 285": "OD1" <-> "OD2" Residue "L PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 8": "OD1" <-> "OD2" Residue "M PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "M GLU 134": "OE1" <-> "OE2" Residue "N ASP 2": "OD1" <-> "OD2" Residue "N GLU 3": "OE1" <-> "OE2" Residue "N PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 128": "OE1" <-> "OE2" Residue "N TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 151": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 136": "OD1" <-> "OD2" Residue "O PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 249": "OD1" <-> "OD2" Residue "O PHE 287": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 129": "OE1" <-> "OE2" Residue "P GLU 143": "OE1" <-> "OE2" Residue "P GLU 149": "OE1" <-> "OE2" Residue "P GLU 189": "OE1" <-> "OE2" Residue "P TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 217": "OE1" <-> "OE2" Residue "P GLU 228": "OE1" <-> "OE2" Residue "P ASP 229": "OD1" <-> "OD2" Residue "P GLU 248": "OE1" <-> "OE2" Residue "P GLU 276": "OE1" <-> "OE2" Residue "Q GLU 122": "OE1" <-> "OE2" Residue "Q ASP 133": "OD1" <-> "OD2" Residue "Q ASP 163": "OD1" <-> "OD2" Residue "Q GLU 192": "OE1" <-> "OE2" Residue "Q GLU 193": "OE1" <-> "OE2" Residue "Q GLU 195": "OE1" <-> "OE2" Residue "Q ASP 243": "OD1" <-> "OD2" Residue "Q ASP 266": "OD1" <-> "OD2" Residue "U PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 287": "OE1" <-> "OE2" Residue "U TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 342": "OD1" <-> "OD2" Residue "U GLU 346": "OE1" <-> "OE2" Residue "U ASP 367": "OD1" <-> "OD2" Residue "U ASP 383": "OD1" <-> "OD2" Residue "U GLU 412": "OE1" <-> "OE2" Residue "R ASP 84": "OD1" <-> "OD2" Residue "R GLU 118": "OE1" <-> "OE2" Residue "R ASP 167": "OD1" <-> "OD2" Residue "R TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 467": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 2": "OE1" <-> "OE2" Residue "S GLU 8": "OE1" <-> "OE2" Residue "S GLU 9": "OE1" <-> "OE2" Residue "S GLU 33": "OE1" <-> "OE2" Residue "S ASP 37": "OD1" <-> "OD2" Residue "S GLU 39": "OE1" <-> "OE2" Residue "S GLU 52": "OE1" <-> "OE2" Residue "S GLU 59": "OE1" <-> "OE2" Residue "S TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 102": "OE1" <-> "OE2" Residue "S GLU 109": "OE1" <-> "OE2" Residue "S ASP 120": "OD1" <-> "OD2" Residue "X PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 33": "OE1" <-> "OE2" Residue "X ASP 59": "OD1" <-> "OD2" Residue "X ASP 61": "OD1" <-> "OD2" Residue "X GLU 64": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 26871 Number of models: 1 Model: "" Number of chains: 18 Chain: "H" Number of atoms: 1652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1652 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "I" Number of atoms: 5014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 622, 5014 Classifications: {'peptide': 622} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 21, 'TRANS': 600} Chain breaks: 5 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 Chain: "J" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 849 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "K" Number of atoms: 1922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1922 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 10, 'TRANS': 222} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 10 Chain: "L" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2502 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 299} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 1325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1325 Classifications: {'peptide': 172} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 164} Chain: "N" Number of atoms: 2613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2613 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "O" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1642 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 201} Chain breaks: 2 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "P" Number of atoms: 1788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1788 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "Q" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1526 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1365 Classifications: {'peptide': 166} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 161} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Chain breaks: 1 Chain: "T" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 915 Classifications: {'peptide': 112} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 104} Chain: "W" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 704 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain: "S" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 982 Classifications: {'peptide': 120} Link IDs: {'TRANS': 119} Chain: "X" Number of atoms: 590 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 590 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 1, 'TRANS': 72} Chain: "i" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 832 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 14.33, per 1000 atoms: 0.53 Number of scatterers: 26871 At special positions: 0 Unit cell: (136.48, 203.014, 196.19, 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) S 139 16.00 P 82 15.00 O 5128 8.00 N 4596 7.00 C 16926 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: 11.35 Conformation dependent library (CDL) restraints added in 5.0 seconds 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6072 Finding SS restraints... Secondary structure from input PDB file: 119 helices and 15 sheets defined 64.6% alpha, 9.6% beta 37 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 8.99 Creating SS restraints... Processing helix chain 'H' and resid 35 through 65 removed outlier: 3.895A pdb=" N ARG H 39 " --> pdb=" O CYS H 35 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN H 52 " --> pdb=" O ALA H 48 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLU H 65 " --> pdb=" O VAL H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 114 removed outlier: 4.300A pdb=" N ALA H 80 " --> pdb=" O LYS H 76 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LYS H 81 " --> pdb=" O GLN H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 122 removed outlier: 3.935A pdb=" N GLN H 122 " --> pdb=" O LYS H 118 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 188 removed outlier: 3.906A pdb=" N LYS H 138 " --> pdb=" O LEU H 134 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LEU H 139 " --> pdb=" O GLU H 135 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP H 156 " --> pdb=" O GLU H 152 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER H 170 " --> pdb=" O GLN H 166 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASP H 185 " --> pdb=" O LYS H 181 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU H 186 " --> pdb=" O GLN H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 223 removed outlier: 4.339A pdb=" N GLN H 200 " --> pdb=" O LYS H 196 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ASN H 201 " --> pdb=" O ILE H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 240 removed outlier: 3.811A pdb=" N ILE H 236 " --> pdb=" O ALA H 232 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 76 Processing helix chain 'I' and resid 82 through 102 removed outlier: 3.620A pdb=" N LYS I 86 " --> pdb=" O GLN I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 removed outlier: 4.608A pdb=" N ASP I 110 " --> pdb=" O SER I 106 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLY I 119 " --> pdb=" O ILE I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 132 removed outlier: 4.681A pdb=" N ARG I 128 " --> pdb=" O ALA I 124 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE I 129 " --> pdb=" O VAL I 125 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU I 130 " --> pdb=" O ASN I 126 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LYS I 131 " --> pdb=" O THR I 127 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 154 removed outlier: 3.871A pdb=" N VAL I 144 " --> pdb=" O SER I 140 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY I 154 " --> pdb=" O TRP I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 171 Processing helix chain 'I' and resid 178 through 183 Processing helix chain 'I' and resid 184 through 190 removed outlier: 3.627A pdb=" N PHE I 188 " --> pdb=" O LEU I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 194 removed outlier: 3.612A pdb=" N ASP I 194 " --> pdb=" O SER I 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 191 through 194' Processing helix chain 'I' and resid 197 through 209 removed outlier: 3.538A pdb=" N LEU I 207 " --> pdb=" O HIS I 203 " (cutoff:3.500A) Processing helix chain 'I' and resid 215 through 230 Processing helix chain 'I' and resid 232 through 246 removed outlier: 3.825A pdb=" N LEU I 238 " --> pdb=" O HIS I 234 " (cutoff:3.500A) Processing helix chain 'I' and resid 269 through 281 Processing helix chain 'I' and resid 328 through 333 removed outlier: 3.605A pdb=" N CYS I 332 " --> pdb=" O SER I 328 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU I 333 " --> pdb=" O LEU I 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 328 through 333' Processing helix chain 'I' and resid 346 through 353 Processing helix chain 'I' and resid 362 through 368 removed outlier: 3.673A pdb=" N ASN I 368 " --> pdb=" O SER I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 369 through 377 removed outlier: 3.590A pdb=" N TYR I 375 " --> pdb=" O LEU I 371 " (cutoff:3.500A) Processing helix chain 'I' and resid 381 through 400 Processing helix chain 'I' and resid 411 through 427 removed outlier: 3.727A pdb=" N PHE I 427 " --> pdb=" O ARG I 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 428 through 430 No H-bonds generated for 'chain 'I' and resid 428 through 430' Processing helix chain 'I' and resid 432 through 443 removed outlier: 3.637A pdb=" N GLU I 436 " --> pdb=" O PHE I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 461 removed outlier: 3.519A pdb=" N SER I 460 " --> pdb=" O LEU I 456 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TRP I 461 " --> pdb=" O GLN I 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 483 Proline residue: I 472 - end of helix removed outlier: 4.927A pdb=" N ASP I 476 " --> pdb=" O PRO I 472 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N HIS I 477 " --> pdb=" O LEU I 473 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 510 removed outlier: 3.906A pdb=" N MET I 510 " --> pdb=" O LEU I 506 " (cutoff:3.500A) Processing helix chain 'I' and resid 511 through 514 Processing helix chain 'I' and resid 525 through 551 removed outlier: 3.750A pdb=" N ASN I 531 " --> pdb=" O GLY I 527 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER I 532 " --> pdb=" O GLY I 528 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL I 533 " --> pdb=" O SER I 529 " (cutoff:3.500A) Processing helix chain 'I' and resid 554 through 569 removed outlier: 3.963A pdb=" N PHE I 560 " --> pdb=" O PHE I 556 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS I 567 " --> pdb=" O ASP I 563 " (cutoff:3.500A) Processing helix chain 'I' and resid 570 through 575 Processing helix chain 'I' and resid 584 through 593 removed outlier: 3.578A pdb=" N LEU I 593 " --> pdb=" O TYR I 589 " (cutoff:3.500A) Processing helix chain 'I' and resid 596 through 625 removed outlier: 3.708A pdb=" N LEU I 600 " --> pdb=" O ASP I 596 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS I 619 " --> pdb=" O THR I 615 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASN I 620 " --> pdb=" O ALA I 616 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LEU I 622 " --> pdb=" O LYS I 618 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N VAL I 623 " --> pdb=" O LYS I 619 " (cutoff:3.500A) Processing helix chain 'I' and resid 633 through 652 removed outlier: 3.961A pdb=" N TYR I 637 " --> pdb=" O SER I 633 " (cutoff:3.500A) Processing helix chain 'I' and resid 664 through 672 removed outlier: 4.219A pdb=" N LEU I 668 " --> pdb=" O ASP I 664 " (cutoff:3.500A) Processing helix chain 'I' and resid 688 through 697 Processing helix chain 'I' and resid 719 through 727 removed outlier: 3.558A pdb=" N GLY I 727 " --> pdb=" O LEU I 723 " (cutoff:3.500A) Processing helix chain 'I' and resid 728 through 740 removed outlier: 3.545A pdb=" N HIS I 740 " --> pdb=" O ARG I 736 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 43 Processing helix chain 'K' and resid 55 through 76 removed outlier: 3.610A pdb=" N SER K 72 " --> pdb=" O THR K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 149 removed outlier: 3.975A pdb=" N GLN K 102 " --> pdb=" O GLN K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 188 Processing helix chain 'K' and resid 211 through 226 removed outlier: 3.514A pdb=" N MET K 215 " --> pdb=" O THR K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 239 through 249 Processing helix chain 'L' and resid 27 through 37 Processing helix chain 'L' and resid 60 through 68 Processing helix chain 'L' and resid 88 through 104 Processing helix chain 'L' and resid 167 through 172 removed outlier: 3.806A pdb=" N GLU L 172 " --> pdb=" O ASP L 168 " (cutoff:3.500A) Processing helix chain 'L' and resid 189 through 205 removed outlier: 3.591A pdb=" N ILE L 195 " --> pdb=" O SER L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 214 through 227 Processing helix chain 'L' and resid 257 through 269 removed outlier: 3.627A pdb=" N VAL L 268 " --> pdb=" O LEU L 264 " (cutoff:3.500A) Processing helix chain 'L' and resid 276 through 296 removed outlier: 3.736A pdb=" N LEU L 287 " --> pdb=" O PHE L 283 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N HIS L 294 " --> pdb=" O HIS L 290 " (cutoff:3.500A) Processing helix chain 'L' and resid 298 through 302 removed outlier: 3.543A pdb=" N THR L 302 " --> pdb=" O LEU L 299 " (cutoff:3.500A) Processing helix chain 'L' and resid 327 through 344 removed outlier: 3.697A pdb=" N VAL L 331 " --> pdb=" O TYR L 327 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 37 Processing helix chain 'M' and resid 74 through 85 removed outlier: 3.934A pdb=" N LEU M 78 " --> pdb=" O SER M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 94 removed outlier: 3.844A pdb=" N LEU M 94 " --> pdb=" O SER M 91 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 110 Processing helix chain 'M' and resid 113 through 124 removed outlier: 3.875A pdb=" N VAL M 117 " --> pdb=" O HIS M 113 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N TYR M 124 " --> pdb=" O LEU M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 135 through 154 removed outlier: 3.706A pdb=" N THR M 141 " --> pdb=" O GLY M 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 161 through 169 removed outlier: 3.615A pdb=" N SER M 167 " --> pdb=" O LEU M 163 " (cutoff:3.500A) Processing helix chain 'N' and resid 3 through 16 Processing helix chain 'N' and resid 20 through 29 Processing helix chain 'N' and resid 32 through 36 Processing helix chain 'N' and resid 44 through 59 Processing helix chain 'N' and resid 62 through 78 removed outlier: 4.184A pdb=" N ALA N 66 " --> pdb=" O SER N 62 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 116 removed outlier: 3.770A pdb=" N LEU N 112 " --> pdb=" O PHE N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 183 Processing helix chain 'N' and resid 197 through 206 Processing helix chain 'N' and resid 241 through 257 Processing helix chain 'N' and resid 325 through 330 Processing helix chain 'O' and resid 17 through 27 removed outlier: 3.681A pdb=" N GLN O 27 " --> pdb=" O ARG O 23 " (cutoff:3.500A) Processing helix chain 'O' and resid 90 through 109 Processing helix chain 'O' and resid 160 through 169 removed outlier: 3.961A pdb=" N ILE O 164 " --> pdb=" O PRO O 160 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 200 Processing helix chain 'O' and resid 261 through 278 removed outlier: 3.969A pdb=" N GLU O 265 " --> pdb=" O SER O 261 " (cutoff:3.500A) Processing helix chain 'O' and resid 279 through 288 removed outlier: 3.568A pdb=" N VAL O 283 " --> pdb=" O PRO O 279 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE O 284 " --> pdb=" O LEU O 280 " (cutoff:3.500A) Processing helix chain 'P' and resid 54 through 75 Processing helix chain 'P' and resid 147 through 161 removed outlier: 3.746A pdb=" N SER P 151 " --> pdb=" O CYS P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 191 removed outlier: 3.611A pdb=" N HIS P 186 " --> pdb=" O ARG P 182 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU P 187 " --> pdb=" O THR P 183 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU P 189 " --> pdb=" O LYS P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 243 through 250 removed outlier: 3.919A pdb=" N LEU P 247 " --> pdb=" O PRO P 243 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 267 Processing helix chain 'P' and resid 271 through 283 Processing helix chain 'Q' and resid 77 through 98 removed outlier: 3.820A pdb=" N ARG Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN Q 98 " --> pdb=" O THR Q 94 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 124 removed outlier: 3.919A pdb=" N ILE Q 106 " --> pdb=" O GLU Q 102 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN Q 107 " --> pdb=" O LYS Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 136 through 197 removed outlier: 3.881A pdb=" N GLU Q 191 " --> pdb=" O ALA Q 187 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N GLU Q 192 " --> pdb=" O SER Q 188 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU Q 193 " --> pdb=" O GLU Q 189 " (cutoff:3.500A) Processing helix chain 'Q' and resid 215 through 220 Processing helix chain 'Q' and resid 223 through 232 removed outlier: 3.882A pdb=" N GLU Q 227 " --> pdb=" O THR Q 223 " (cutoff:3.500A) Processing helix chain 'Q' and resid 234 through 248 removed outlier: 5.469A pdb=" N ASP Q 241 " --> pdb=" O ALA Q 237 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N ILE Q 244 " --> pdb=" O LYS Q 240 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 268 removed outlier: 3.738A pdb=" N LYS Q 252 " --> pdb=" O SER Q 248 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N SER Q 268 " --> pdb=" O LYS Q 264 " (cutoff:3.500A) Processing helix chain 'U' and resid 253 through 267 removed outlier: 4.256A pdb=" N GLU U 257 " --> pdb=" O ILE U 253 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS U 262 " --> pdb=" O PHE U 258 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N LEU U 263 " --> pdb=" O GLU U 259 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLN U 267 " --> pdb=" O LEU U 263 " (cutoff:3.500A) Processing helix chain 'U' and resid 271 through 369 removed outlier: 4.197A pdb=" N GLN U 318 " --> pdb=" O GLU U 314 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG U 319 " --> pdb=" O LYS U 315 " (cutoff:3.500A) Proline residue: U 332 - end of helix removed outlier: 4.169A pdb=" N GLU U 346 " --> pdb=" O ASP U 342 " (cutoff:3.500A) Processing helix chain 'U' and resid 370 through 375 removed outlier: 4.061A pdb=" N GLU U 375 " --> pdb=" O VAL U 371 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 385 No H-bonds generated for 'chain 'U' and resid 383 through 385' Processing helix chain 'U' and resid 386 through 399 removed outlier: 4.506A pdb=" N THR U 396 " --> pdb=" O PHE U 392 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU U 397 " --> pdb=" O LYS U 393 " (cutoff:3.500A) Processing helix chain 'U' and resid 399 through 415 Processing helix chain 'R' and resid 85 through 105 removed outlier: 4.236A pdb=" N GLU R 98 " --> pdb=" O GLU R 94 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLU R 99 " --> pdb=" O LYS R 95 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 114 removed outlier: 3.666A pdb=" N GLU R 114 " --> pdb=" O ILE R 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 124 removed outlier: 3.847A pdb=" N GLU R 120 " --> pdb=" O SER R 116 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU R 122 " --> pdb=" O GLU R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 131 through 150 removed outlier: 4.337A pdb=" N LYS R 140 " --> pdb=" O MET R 136 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU R 141 " --> pdb=" O GLN R 137 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU R 142 " --> pdb=" O LYS R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 177 removed outlier: 4.024A pdb=" N ILE R 175 " --> pdb=" O PHE R 171 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU R 176 " --> pdb=" O LEU R 172 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASN R 177 " --> pdb=" O LYS R 173 " (cutoff:3.500A) Processing helix chain 'T' and resid 454 through 472 removed outlier: 4.341A pdb=" N HIS T 462 " --> pdb=" O ALA T 458 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N TYR T 463 " --> pdb=" O GLY T 459 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LYS T 472 " --> pdb=" O SER T 468 " (cutoff:3.500A) Processing helix chain 'T' and resid 478 through 506 removed outlier: 4.158A pdb=" N MET T 482 " --> pdb=" O LYS T 478 " (cutoff:3.500A) Processing helix chain 'T' and resid 511 through 522 removed outlier: 3.657A pdb=" N LEU T 515 " --> pdb=" O LYS T 511 " (cutoff:3.500A) Processing helix chain 'T' and resid 530 through 539 removed outlier: 3.776A pdb=" N LEU T 534 " --> pdb=" O SER T 530 " (cutoff:3.500A) Processing helix chain 'T' and resid 540 through 548 removed outlier: 3.942A pdb=" N LEU T 546 " --> pdb=" O GLU T 542 " (cutoff:3.500A) Processing helix chain 'W' and resid 18 through 30 Processing helix chain 'W' and resid 38 through 65 removed outlier: 3.743A pdb=" N LEU W 42 " --> pdb=" O SER W 38 " (cutoff:3.500A) Processing helix chain 'W' and resid 71 through 87 removed outlier: 3.630A pdb=" N VAL W 75 " --> pdb=" O ASN W 71 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL W 81 " --> pdb=" O ALA W 77 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N LYS W 84 " --> pdb=" O LYS W 80 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG W 87 " --> pdb=" O LEU W 83 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 37 removed outlier: 4.163A pdb=" N LEU S 36 " --> pdb=" O GLU S 32 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASP S 37 " --> pdb=" O GLU S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 72 removed outlier: 3.818A pdb=" N GLU S 59 " --> pdb=" O PHE S 55 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN S 60 " --> pdb=" O ARG S 56 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA S 72 " --> pdb=" O PHE S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 78 through 86 removed outlier: 3.687A pdb=" N VAL S 82 " --> pdb=" O ASN S 78 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA S 86 " --> pdb=" O VAL S 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 89 through 120 Processing helix chain 'X' and resid 4 through 15 removed outlier: 3.512A pdb=" N VAL X 8 " --> pdb=" O ARG X 4 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N HIS X 15 " --> pdb=" O LEU X 11 " (cutoff:3.500A) Processing helix chain 'X' and resid 24 through 54 removed outlier: 3.564A pdb=" N VAL X 32 " --> pdb=" O LEU X 28 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU X 33 " --> pdb=" O GLN X 29 " (cutoff:3.500A) Processing helix chain 'X' and resid 59 through 74 removed outlier: 3.691A pdb=" N VAL X 66 " --> pdb=" O GLN X 62 " (cutoff:3.500A) Proline residue: X 68 - end of helix removed outlier: 3.563A pdb=" N LEU X 71 " --> pdb=" O LEU X 67 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 250 through 251 Processing sheet with id=AA2, first strand: chain 'K' and resid 232 through 233 Processing sheet with id=AA3, first strand: chain 'L' and resid 47 through 48 Processing sheet with id=AA4, first strand: chain 'L' and resid 117 through 123 removed outlier: 7.079A pdb=" N PHE L 137 " --> pdb=" O TRP L 161 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP L 161 " --> pdb=" O PHE L 137 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL L 139 " --> pdb=" O THR L 159 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR L 159 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE L 141 " --> pdb=" O LEU L 157 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 117 through 123 removed outlier: 7.079A pdb=" N PHE L 137 " --> pdb=" O TRP L 161 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP L 161 " --> pdb=" O PHE L 137 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N VAL L 139 " --> pdb=" O THR L 159 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N THR L 159 " --> pdb=" O VAL L 139 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE L 141 " --> pdb=" O LEU L 157 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS L 319 " --> pdb=" O HIS L 315 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N LEU L 240 " --> pdb=" O VAL L 305 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL L 307 " --> pdb=" O GLU L 238 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU L 238 " --> pdb=" O VAL L 307 " (cutoff:3.500A) removed outlier: 10.581A pdb=" N LEU N 294 " --> pdb=" O GLU N 272 " (cutoff:3.500A) removed outlier: 10.106A pdb=" N GLU N 272 " --> pdb=" O LEU N 294 " (cutoff:3.500A) removed outlier: 9.771A pdb=" N LYS N 296 " --> pdb=" O LYS N 270 " (cutoff:3.500A) removed outlier: 10.099A pdb=" N LYS N 270 " --> pdb=" O LYS N 296 " (cutoff:3.500A) removed outlier: 10.061A pdb=" N SER N 298 " --> pdb=" O GLN N 268 " (cutoff:3.500A) removed outlier: 10.190A pdb=" N GLN N 268 " --> pdb=" O SER N 298 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N PHE N 266 " --> pdb=" O PRO N 300 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU N 264 " --> pdb=" O LEU N 302 " (cutoff:3.500A) removed outlier: 9.038A pdb=" N PHE N 334 " --> pdb=" O PHE N 266 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLN N 268 " --> pdb=" O PHE N 334 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ILE N 336 " --> pdb=" O GLN N 268 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS N 270 " --> pdb=" O ILE N 336 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 80 through 81 Processing sheet with id=AA7, first strand: chain 'M' and resid 128 through 130 removed outlier: 6.477A pdb=" N ILE M 66 " --> pdb=" O CYS M 98 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N LEU M 100 " --> pdb=" O ILE M 66 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N PHE M 68 " --> pdb=" O LEU M 100 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N THR M 102 " --> pdb=" O PHE M 68 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL M 70 " --> pdb=" O THR M 102 " (cutoff:3.500A) removed outlier: 9.519A pdb=" N LEU M 65 " --> pdb=" O THR M 15 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR M 17 " --> pdb=" O LEU M 65 " (cutoff:3.500A) removed outlier: 8.647A pdb=" N VAL M 67 " --> pdb=" O THR M 17 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU M 19 " --> pdb=" O VAL M 67 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL M 69 " --> pdb=" O LEU M 19 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N VAL M 21 " --> pdb=" O VAL M 69 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ASN M 71 " --> pdb=" O VAL M 21 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N ILE N 238 " --> pdb=" O LEU M 44 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL M 46 " --> pdb=" O ILE N 238 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 120 through 126 removed outlier: 4.687A pdb=" N TYR N 151 " --> pdb=" O SER N 164 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N TYR N 155 " --> pdb=" O TYR N 160 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N TYR N 160 " --> pdb=" O TYR N 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA N 161 " --> pdb=" O PHE N 86 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL N 85 " --> pdb=" O LEU N 193 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N LEU N 193 " --> pdb=" O VAL N 85 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLN N 87 " --> pdb=" O MET N 191 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N MET N 191 " --> pdb=" O GLN N 87 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N SER N 89 " --> pdb=" O VAL N 189 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N VAL N 189 " --> pdb=" O SER N 89 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 113 through 117 removed outlier: 3.773A pdb=" N VAL O 122 " --> pdb=" O LEU O 142 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N THR O 128 " --> pdb=" O ASP O 136 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASP O 136 " --> pdb=" O THR O 128 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N PHE O 130 " --> pdb=" O LEU O 134 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LEU O 134 " --> pdb=" O PHE O 130 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N HIS O 152 " --> pdb=" O ASP O 141 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N VAL O 143 " --> pdb=" O ILE O 150 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ILE O 150 " --> pdb=" O VAL O 143 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'O' and resid 217 through 224 removed outlier: 3.883A pdb=" N LEU O 224 " --> pdb=" O PHE O 231 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE O 231 " --> pdb=" O LEU O 224 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'P' and resid 77 through 87 removed outlier: 5.139A pdb=" N SER P 108 " --> pdb=" O ARG P 79 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N HIS P 81 " --> pdb=" O ARG P 106 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ARG P 106 " --> pdb=" O HIS P 81 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS P 83 " --> pdb=" O ARG P 104 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ARG P 104 " --> pdb=" O LYS P 83 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N THR P 85 " --> pdb=" O LEU P 102 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU P 102 " --> pdb=" O THR P 85 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ASP P 87 " --> pdb=" O LYS P 100 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LYS P 100 " --> pdb=" O ASP P 87 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N THR P 115 " --> pdb=" O MET P 142 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N MET P 142 " --> pdb=" O THR P 115 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N GLN P 117 " --> pdb=" O ILE P 140 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ILE P 140 " --> pdb=" O GLN P 117 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLU P 119 " --> pdb=" O LEU P 138 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU P 138 " --> pdb=" O GLU P 119 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLN P 121 " --> pdb=" O THR P 136 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA P 134 " --> pdb=" O LEU P 123 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 195 through 196 removed outlier: 3.620A pdb=" N GLY P 207 " --> pdb=" O TYR P 196 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU P 217 " --> pdb=" O LYS P 241 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS P 241 " --> pdb=" O GLU P 217 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'T' and resid 475 through 476 Processing sheet with id=AB5, first strand: chain 'T' and resid 550 through 552 Processing sheet with id=AB6, first strand: chain 'S' and resid 76 through 77 1569 hydrogen bonds defined for protein. 4605 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 92 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 9.27 Time building geometry restraints manager: 12.17 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: 4252 1.31 - 1.43: 7236 1.43 - 1.56: 15661 1.56 - 1.68: 162 1.68 - 1.81: 216 Bond restraints: 27527 Sorted by residual: bond pdb=" CA LYS L 70 " pdb=" C LYS L 70 " ideal model delta sigma weight residual 1.522 1.466 0.056 1.24e-02 6.50e+03 2.03e+01 bond pdb=" C TRP L 72 " pdb=" O TRP L 72 " ideal model delta sigma weight residual 1.235 1.180 0.055 1.23e-02 6.61e+03 2.02e+01 bond pdb=" C GLN L 71 " pdb=" O GLN L 71 " ideal model delta sigma weight residual 1.236 1.187 0.049 1.21e-02 6.83e+03 1.64e+01 bond pdb=" CA GLN L 71 " pdb=" C GLN L 71 " ideal model delta sigma weight residual 1.523 1.475 0.048 1.23e-02 6.61e+03 1.54e+01 bond pdb=" C1' DG J 15 " pdb=" N9 DG J 15 " ideal model delta sigma weight residual 1.460 1.389 0.071 2.00e-02 2.50e+03 1.28e+01 ... (remaining 27522 not shown) Histogram of bond angle deviations from ideal: 99.52 - 106.43: 1086 106.43 - 113.35: 15273 113.35 - 120.26: 10247 120.26 - 127.18: 10453 127.18 - 134.09: 415 Bond angle restraints: 37474 Sorted by residual: angle pdb=" O3' DA i 17 " pdb=" C3' DA i 17 " pdb=" C2' DA i 17 " ideal model delta sigma weight residual 111.50 101.96 9.54 1.50e+00 4.44e-01 4.05e+01 angle pdb=" N GLU N 128 " pdb=" CA GLU N 128 " pdb=" C GLU N 128 " ideal model delta sigma weight residual 113.56 106.25 7.31 1.39e+00 5.18e-01 2.77e+01 angle pdb=" CA HIS L 69 " pdb=" C HIS L 69 " pdb=" N LYS L 70 " ideal model delta sigma weight residual 116.21 122.22 -6.01 1.29e+00 6.01e-01 2.17e+01 angle pdb=" O HIS L 69 " pdb=" C HIS L 69 " pdb=" N LYS L 70 " ideal model delta sigma weight residual 122.41 116.55 5.86 1.34e+00 5.57e-01 1.91e+01 angle pdb=" N LYS L 70 " pdb=" CA LYS L 70 " pdb=" C LYS L 70 " ideal model delta sigma weight residual 109.24 102.78 6.46 1.51e+00 4.39e-01 1.83e+01 ... (remaining 37469 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 14757 17.90 - 35.80: 1265 35.80 - 53.70: 486 53.70 - 71.60: 118 71.60 - 89.50: 28 Dihedral angle restraints: 16654 sinusoidal: 7403 harmonic: 9251 Sorted by residual: dihedral pdb=" CA GLN H 122 " pdb=" C GLN H 122 " pdb=" N SER H 123 " pdb=" CA SER H 123 " ideal model delta harmonic sigma weight residual -180.00 -147.51 -32.49 0 5.00e+00 4.00e-02 4.22e+01 dihedral pdb=" CA CYS P 111 " pdb=" C CYS P 111 " pdb=" N HIS P 112 " pdb=" CA HIS P 112 " ideal model delta harmonic sigma weight residual 180.00 155.38 24.62 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA SER H 124 " pdb=" C SER H 124 " pdb=" N VAL H 125 " pdb=" CA VAL H 125 " ideal model delta harmonic sigma weight residual 180.00 155.58 24.42 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 16651 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 3942 0.064 - 0.129: 347 0.129 - 0.193: 9 0.193 - 0.258: 0 0.258 - 0.322: 2 Chirality restraints: 4300 Sorted by residual: chirality pdb=" C3' DA i 17 " pdb=" C4' DA i 17 " pdb=" O3' DA i 17 " pdb=" C2' DA i 17 " both_signs ideal model delta sigma weight residual False -2.66 -2.98 0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CB ILE K 82 " pdb=" CA ILE K 82 " pdb=" CG1 ILE K 82 " pdb=" CG2 ILE K 82 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C3' DT J 3 " pdb=" C4' DT J 3 " pdb=" O3' DT J 3 " pdb=" C2' DT J 3 " both_signs ideal model delta sigma weight residual False -2.66 -2.84 0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 4297 not shown) Planarity restraints: 4432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS P 111 " 0.012 2.00e-02 2.50e+03 2.47e-02 6.10e+00 pdb=" C CYS P 111 " -0.043 2.00e-02 2.50e+03 pdb=" O CYS P 111 " 0.016 2.00e-02 2.50e+03 pdb=" N HIS P 112 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA i 16 " -0.025 2.00e-02 2.50e+03 1.26e-02 4.34e+00 pdb=" N9 DA i 16 " 0.017 2.00e-02 2.50e+03 pdb=" C8 DA i 16 " 0.011 2.00e-02 2.50e+03 pdb=" N7 DA i 16 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA i 16 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DA i 16 " -0.011 2.00e-02 2.50e+03 pdb=" N6 DA i 16 " 0.002 2.00e-02 2.50e+03 pdb=" N1 DA i 16 " -0.015 2.00e-02 2.50e+03 pdb=" C2 DA i 16 " 0.017 2.00e-02 2.50e+03 pdb=" N3 DA i 16 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DA i 16 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT i 21 " -0.024 2.00e-02 2.50e+03 1.19e-02 3.55e+00 pdb=" N1 DT i 21 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DT i 21 " 0.006 2.00e-02 2.50e+03 pdb=" O2 DT i 21 " 0.013 2.00e-02 2.50e+03 pdb=" N3 DT i 21 " 0.001 2.00e-02 2.50e+03 pdb=" C4 DT i 21 " -0.004 2.00e-02 2.50e+03 pdb=" O4 DT i 21 " -0.018 2.00e-02 2.50e+03 pdb=" C5 DT i 21 " 0.007 2.00e-02 2.50e+03 pdb=" C7 DT i 21 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DT i 21 " 0.015 2.00e-02 2.50e+03 ... (remaining 4429 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.30: 22 2.30 - 2.95: 11199 2.95 - 3.60: 39754 3.60 - 4.25: 59170 4.25 - 4.90: 99120 Nonbonded interactions: 209265 Sorted by model distance: nonbonded pdb=" N3 DG J 5 " pdb=" N2 DG i -3 " model vdw 1.653 2.600 nonbonded pdb=" C2' DA i 20 " pdb=" C7 DT i 21 " model vdw 1.767 3.860 nonbonded pdb=" N1 DG J 5 " pdb=" N1 DG i -3 " model vdw 1.772 3.200 nonbonded pdb=" C2 DG J 5 " pdb=" N2 DG i -3 " model vdw 1.832 3.340 nonbonded pdb=" C2 DG J 5 " pdb=" C2 DG i -3 " model vdw 1.919 3.480 ... (remaining 209260 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.190 Construct map_model_manager: 0.020 Extract box with map and model: 18.500 Check model and map are aligned: 0.490 Set scattering table: 0.240 Process input model: 76.820 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.100 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:12.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 113.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7333 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 27527 Z= 0.181 Angle : 0.510 9.542 37474 Z= 0.302 Chirality : 0.037 0.322 4300 Planarity : 0.003 0.044 4432 Dihedral : 16.184 89.496 10582 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.61 % Favored : 97.32 % Rotamer: Outliers : 0.82 % Allowed : 8.35 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.67 (0.14), residues: 3064 helix: 0.27 (0.11), residues: 1899 sheet: -0.32 (0.29), residues: 307 loop : -1.96 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP L 72 HIS 0.003 0.000 HIS P 112 PHE 0.013 0.001 PHE I 482 TYR 0.012 0.001 TYR O 239 ARG 0.003 0.000 ARG S 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 333 time to evaluate : 3.234 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: Q 93 MET cc_start: 0.8997 (ttp) cc_final: 0.8670 (tmt) REVERT: U 289 PHE cc_start: 0.8464 (m-10) cc_final: 0.8048 (m-80) REVERT: U 383 ASP cc_start: 0.7612 (p0) cc_final: 0.7198 (p0) REVERT: U 406 ASN cc_start: 0.8736 (m-40) cc_final: 0.8368 (m-40) REVERT: R 86 PHE cc_start: 0.4342 (m-80) cc_final: 0.4071 (m-10) REVERT: R 87 MET cc_start: 0.7825 (mmm) cc_final: 0.7463 (mmp) REVERT: T 478 LYS cc_start: 0.9017 (mmmt) cc_final: 0.8747 (mmmm) REVERT: S 13 PHE cc_start: 0.8452 (t80) cc_final: 0.7881 (t80) REVERT: S 57 GLN cc_start: 0.7745 (tp40) cc_final: 0.7141 (tm-30) REVERT: X 5 LYS cc_start: 0.8171 (mmmm) cc_final: 0.7589 (mmtt) REVERT: X 6 GLU cc_start: 0.6962 (tp30) cc_final: 0.6644 (tp30) REVERT: X 41 GLU cc_start: 0.8466 (tp30) cc_final: 0.7903 (tp30) REVERT: X 49 GLN cc_start: 0.9305 (tm-30) cc_final: 0.8872 (tm-30) REVERT: X 69 GLN cc_start: 0.8979 (tm-30) cc_final: 0.8702 (tm-30) outliers start: 23 outliers final: 10 residues processed: 350 average time/residue: 1.8306 time to fit residues: 719.0147 Evaluate side-chains 241 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 231 time to evaluate : 3.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 224 ASP Chi-restraints excluded: chain I residue 331 ASP Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain Q residue 108 TYR Chi-restraints excluded: chain U residue 329 ARG Chi-restraints excluded: chain S residue 51 SER Chi-restraints excluded: chain X residue 59 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 266 optimal weight: 7.9990 chunk 239 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 161 optimal weight: 5.9990 chunk 127 optimal weight: 0.0570 chunk 247 optimal weight: 10.0000 chunk 95 optimal weight: 0.7980 chunk 150 optimal weight: 7.9990 chunk 184 optimal weight: 4.9990 chunk 286 optimal weight: 0.0470 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 132 HIS H 182 GLN H 191 ASN H 203 GLN H 213 GLN I 97 ASN I 193 GLN I 236 GLN I 349 GLN I 352 GLN I 374 HIS I 394 GLN I 429 GLN I 726 GLN L 51 GLN L 201 GLN L 294 HIS M 156 HIS N 78 GLN N 80 GLN N 185 HIS O 106 GLN O 198 GLN O 267 GLN P 59 GLN P 105 HIS P 112 HIS Q 111 ASN Q 177 GLN Q 181 ASN Q 202 GLN Q 204 ASN U 406 ASN R 130 HIS R 147 ASN T 456 HIS ** T 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 555 ASN X 29 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 27527 Z= 0.171 Angle : 0.524 10.914 37474 Z= 0.276 Chirality : 0.037 0.213 4300 Planarity : 0.004 0.051 4432 Dihedral : 16.288 121.120 4233 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.99 % Allowed : 13.83 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.15), residues: 3064 helix: 1.39 (0.12), residues: 1926 sheet: 0.05 (0.29), residues: 304 loop : -1.40 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 718 HIS 0.016 0.001 HIS P 112 PHE 0.027 0.001 PHE O 287 TYR 0.016 0.001 TYR U 356 ARG 0.012 0.000 ARG X 48 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 262 time to evaluate : 3.313 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: O 25 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7531 (tt0) REVERT: Q 93 MET cc_start: 0.8998 (ttp) cc_final: 0.8664 (tmt) REVERT: U 383 ASP cc_start: 0.7641 (p0) cc_final: 0.7323 (p0) REVERT: U 406 ASN cc_start: 0.8743 (m110) cc_final: 0.8457 (m-40) REVERT: R 86 PHE cc_start: 0.4459 (m-80) cc_final: 0.4087 (m-10) REVERT: R 87 MET cc_start: 0.7835 (mmm) cc_final: 0.7479 (mmp) REVERT: R 101 MET cc_start: 0.7374 (OUTLIER) cc_final: 0.7100 (mpt) REVERT: T 476 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7239 (mt-10) REVERT: W 1 MET cc_start: 0.7003 (pmm) cc_final: 0.6657 (pmm) REVERT: S 57 GLN cc_start: 0.7855 (tp40) cc_final: 0.7051 (tm-30) REVERT: S 73 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8717 (mtpt) REVERT: S 83 LYS cc_start: 0.9275 (mtpp) cc_final: 0.9067 (mtmp) REVERT: X 5 LYS cc_start: 0.8087 (mmmm) cc_final: 0.7478 (mmtt) REVERT: X 41 GLU cc_start: 0.8459 (tp30) cc_final: 0.7840 (tp30) REVERT: X 49 GLN cc_start: 0.9358 (tm-30) cc_final: 0.8852 (tm-30) REVERT: X 69 GLN cc_start: 0.8987 (tm-30) cc_final: 0.8603 (tp-100) outliers start: 56 outliers final: 20 residues processed: 300 average time/residue: 1.6826 time to fit residues: 570.7084 Evaluate side-chains 243 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 220 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 331 ASP Chi-restraints excluded: chain I residue 410 HIS Chi-restraints excluded: chain I residue 651 LEU Chi-restraints excluded: chain K residue 135 ILE Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 133 ASP Chi-restraints excluded: chain U residue 329 ARG Chi-restraints excluded: chain R residue 101 MET Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 454 ASP Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain S residue 51 SER Chi-restraints excluded: chain S residue 73 LYS Chi-restraints excluded: chain X residue 59 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 159 optimal weight: 0.8980 chunk 89 optimal weight: 0.0060 chunk 238 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 287 optimal weight: 3.9990 chunk 310 optimal weight: 8.9990 chunk 256 optimal weight: 7.9990 chunk 285 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 chunk 230 optimal weight: 2.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 213 GLN P 112 HIS R 130 HIS T 545 GLN X 29 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 27527 Z= 0.209 Angle : 0.545 9.861 37474 Z= 0.286 Chirality : 0.038 0.191 4300 Planarity : 0.004 0.052 4432 Dihedral : 16.197 79.341 4228 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.13 % Allowed : 15.96 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.35 (0.15), residues: 3064 helix: 1.85 (0.12), residues: 1934 sheet: 0.31 (0.30), residues: 296 loop : -1.16 (0.20), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 718 HIS 0.016 0.001 HIS I 91 PHE 0.025 0.001 PHE O 287 TYR 0.012 0.001 TYR I 565 ARG 0.009 0.001 ARG X 48 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 243 time to evaluate : 3.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 135 PRO cc_start: 0.7040 (Cg_exo) cc_final: 0.6613 (Cg_endo) REVERT: I 171 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7496 (mtt) REVERT: I 514 MET cc_start: 0.5902 (OUTLIER) cc_final: 0.5275 (mpp) REVERT: O 25 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7568 (tt0) REVERT: Q 93 MET cc_start: 0.9021 (ttp) cc_final: 0.8625 (tmt) REVERT: U 383 ASP cc_start: 0.7651 (p0) cc_final: 0.7280 (p0) REVERT: U 406 ASN cc_start: 0.8681 (m110) cc_final: 0.8327 (m-40) REVERT: R 86 PHE cc_start: 0.4608 (m-80) cc_final: 0.4250 (m-10) REVERT: R 87 MET cc_start: 0.7761 (mmm) cc_final: 0.7417 (mmp) REVERT: T 476 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7415 (mt-10) REVERT: W 1 MET cc_start: 0.7201 (pmm) cc_final: 0.6740 (pmm) REVERT: S 57 GLN cc_start: 0.8019 (tp40) cc_final: 0.7300 (tm-30) REVERT: X 5 LYS cc_start: 0.8066 (mmmm) cc_final: 0.6666 (mmtt) REVERT: X 33 GLU cc_start: 0.7466 (tp30) cc_final: 0.7180 (tp30) REVERT: X 45 ARG cc_start: 0.8959 (mmt90) cc_final: 0.8651 (mtt-85) REVERT: X 49 GLN cc_start: 0.9362 (tm-30) cc_final: 0.8872 (tm-30) REVERT: X 64 GLU cc_start: 0.8400 (mp0) cc_final: 0.8108 (mp0) REVERT: X 69 GLN cc_start: 0.8999 (tm-30) cc_final: 0.8594 (tp-100) outliers start: 60 outliers final: 26 residues processed: 286 average time/residue: 1.6776 time to fit residues: 543.2541 Evaluate side-chains 249 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 220 time to evaluate : 3.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 331 ASP Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain I residue 651 LEU Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 248 THR Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 259 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 114 VAL Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 454 ASP Chi-restraints excluded: chain T residue 526 THR Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 51 SER Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain X residue 59 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 284 optimal weight: 6.9990 chunk 216 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 137 optimal weight: 4.9990 chunk 193 optimal weight: 0.3980 chunk 288 optimal weight: 5.9990 chunk 305 optimal weight: 8.9990 chunk 150 optimal weight: 0.9990 chunk 273 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 213 GLN I 114 ASN I 236 GLN P 112 HIS ** U 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 111 GLN R 130 HIS T 545 GLN S 11 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 27527 Z= 0.341 Angle : 0.619 9.971 37474 Z= 0.328 Chirality : 0.041 0.179 4300 Planarity : 0.004 0.054 4432 Dihedral : 16.348 80.069 4224 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.60 % Allowed : 17.56 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.40 (0.15), residues: 3064 helix: 1.87 (0.12), residues: 1939 sheet: 0.30 (0.30), residues: 300 loop : -1.10 (0.21), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 718 HIS 0.016 0.001 HIS I 91 PHE 0.026 0.002 PHE I 583 TYR 0.017 0.002 TYR I 72 ARG 0.006 0.001 ARG S 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 235 time to evaluate : 3.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 135 PRO cc_start: 0.7341 (Cg_exo) cc_final: 0.6824 (Cg_endo) REVERT: I 171 MET cc_start: 0.8167 (OUTLIER) cc_final: 0.7665 (mtt) REVERT: I 514 MET cc_start: 0.5938 (OUTLIER) cc_final: 0.5279 (mpp) REVERT: O 25 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7755 (tp30) REVERT: O 191 LYS cc_start: 0.9061 (OUTLIER) cc_final: 0.8840 (tttm) REVERT: Q 87 MET cc_start: 0.8462 (tpt) cc_final: 0.8027 (tpp) REVERT: Q 93 MET cc_start: 0.9096 (ttp) cc_final: 0.8579 (tmt) REVERT: Q 147 ARG cc_start: 0.8382 (ttm-80) cc_final: 0.8060 (mtp85) REVERT: U 289 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.8185 (m-80) REVERT: U 406 ASN cc_start: 0.8681 (m110) cc_final: 0.8347 (m-40) REVERT: R 87 MET cc_start: 0.7683 (mmm) cc_final: 0.7458 (mmp) REVERT: T 476 GLU cc_start: 0.7843 (mt-10) cc_final: 0.7559 (mt-10) REVERT: T 484 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7974 (mt-10) REVERT: S 17 GLN cc_start: 0.8915 (mm110) cc_final: 0.8710 (mm110) REVERT: X 6 GLU cc_start: 0.7297 (tm-30) cc_final: 0.6688 (tm-30) REVERT: X 33 GLU cc_start: 0.7357 (tp30) cc_final: 0.6922 (tp30) REVERT: X 41 GLU cc_start: 0.8456 (mm-30) cc_final: 0.8140 (tm-30) REVERT: X 45 ARG cc_start: 0.8937 (mmt90) cc_final: 0.8710 (mtt-85) REVERT: X 49 GLN cc_start: 0.9316 (tm-30) cc_final: 0.8767 (tm-30) REVERT: X 64 GLU cc_start: 0.8540 (mp0) cc_final: 0.8108 (mp0) REVERT: X 69 GLN cc_start: 0.9000 (tm-30) cc_final: 0.8487 (tp-100) outliers start: 73 outliers final: 25 residues processed: 286 average time/residue: 1.6212 time to fit residues: 529.0764 Evaluate side-chains 245 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 215 time to evaluate : 3.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 331 ASP Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 191 LYS Chi-restraints excluded: chain O residue 248 THR Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain U residue 289 PHE Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 454 ASP Chi-restraints excluded: chain T residue 526 THR Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain W residue 40 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 51 SER Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain X residue 21 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 254 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 227 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 260 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 155 optimal weight: 3.9990 chunk 274 optimal weight: 0.9980 chunk 77 optimal weight: 0.0970 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 214 HIS M 144 GLN P 112 HIS Q 142 ASN U 284 ASN ** U 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS T 545 GLN S 11 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 27527 Z= 0.230 Angle : 0.574 10.533 37474 Z= 0.301 Chirality : 0.039 0.186 4300 Planarity : 0.004 0.054 4432 Dihedral : 16.269 81.288 4220 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.06 % Allowed : 19.37 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: 1.68 (0.16), residues: 3064 helix: 2.06 (0.12), residues: 1942 sheet: 0.44 (0.30), residues: 300 loop : -0.95 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 718 HIS 0.019 0.001 HIS I 91 PHE 0.024 0.001 PHE O 287 TYR 0.020 0.001 TYR S 25 ARG 0.011 0.000 ARG X 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 233 time to evaluate : 3.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 135 PRO cc_start: 0.7444 (Cg_exo) cc_final: 0.6962 (Cg_endo) REVERT: I 171 MET cc_start: 0.8089 (OUTLIER) cc_final: 0.7635 (mtt) REVERT: I 268 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8108 (tt) REVERT: I 514 MET cc_start: 0.5938 (OUTLIER) cc_final: 0.5271 (mpp) REVERT: O 25 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7667 (tp30) REVERT: P 244 GLN cc_start: 0.5476 (tm-30) cc_final: 0.4697 (tm-30) REVERT: Q 87 MET cc_start: 0.8495 (tpt) cc_final: 0.8128 (tpp) REVERT: Q 93 MET cc_start: 0.9097 (ttp) cc_final: 0.8679 (tmm) REVERT: Q 147 ARG cc_start: 0.8341 (ttm-80) cc_final: 0.8021 (mtp85) REVERT: U 289 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.8203 (m-80) REVERT: U 405 ARG cc_start: 0.8965 (tpp80) cc_final: 0.8582 (tpp80) REVERT: U 406 ASN cc_start: 0.8714 (m110) cc_final: 0.8370 (m-40) REVERT: T 476 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7557 (mt-10) REVERT: W 1 MET cc_start: 0.7156 (pmm) cc_final: 0.6865 (pmm) REVERT: X 5 LYS cc_start: 0.8244 (mmmm) cc_final: 0.7867 (mmtt) REVERT: X 41 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8041 (tm-30) REVERT: X 49 GLN cc_start: 0.9317 (tm-30) cc_final: 0.8838 (tm-30) REVERT: X 64 GLU cc_start: 0.8587 (mp0) cc_final: 0.8115 (mp0) REVERT: X 69 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8563 (tp-100) outliers start: 58 outliers final: 23 residues processed: 274 average time/residue: 1.6475 time to fit residues: 511.3596 Evaluate side-chains 242 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 214 time to evaluate : 3.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 331 ASP Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain Q residue 265 LEU Chi-restraints excluded: chain U residue 289 PHE Chi-restraints excluded: chain R residue 131 PHE Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 454 ASP Chi-restraints excluded: chain T residue 526 THR Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain W residue 40 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 51 SER Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain S residue 90 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 102 optimal weight: 3.9990 chunk 275 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 179 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 305 optimal weight: 7.9990 chunk 253 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 191 ASN P 112 HIS ** U 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS S 11 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 27527 Z= 0.214 Angle : 0.575 10.251 37474 Z= 0.300 Chirality : 0.038 0.185 4300 Planarity : 0.004 0.053 4432 Dihedral : 16.207 81.404 4220 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.45 % Allowed : 20.09 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.81 (0.16), residues: 3064 helix: 2.16 (0.12), residues: 1943 sheet: 0.48 (0.30), residues: 301 loop : -0.88 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 718 HIS 0.019 0.001 HIS I 91 PHE 0.024 0.001 PHE O 287 TYR 0.019 0.001 TYR I 72 ARG 0.006 0.000 ARG X 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 229 time to evaluate : 3.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 60 MET cc_start: 0.6886 (tpp) cc_final: 0.6181 (mpp) REVERT: I 135 PRO cc_start: 0.7437 (Cg_exo) cc_final: 0.6970 (Cg_endo) REVERT: I 171 MET cc_start: 0.8076 (OUTLIER) cc_final: 0.7632 (mtt) REVERT: I 268 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8100 (tt) REVERT: I 514 MET cc_start: 0.6023 (OUTLIER) cc_final: 0.5329 (mpp) REVERT: O 25 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7673 (tp30) REVERT: O 191 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8804 (tttm) REVERT: Q 93 MET cc_start: 0.9098 (ttp) cc_final: 0.8686 (tmm) REVERT: Q 147 ARG cc_start: 0.8351 (ttm-80) cc_final: 0.8073 (mtp85) REVERT: U 289 PHE cc_start: 0.8434 (OUTLIER) cc_final: 0.8202 (m-80) REVERT: U 406 ASN cc_start: 0.8727 (m110) cc_final: 0.8386 (m-40) REVERT: R 104 MET cc_start: 0.7952 (tpt) cc_final: 0.7510 (ptt) REVERT: T 476 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7588 (mt-10) REVERT: T 478 LYS cc_start: 0.9090 (mmmm) cc_final: 0.8748 (mmmm) REVERT: S 67 MET cc_start: 0.8700 (ttp) cc_final: 0.8466 (ttm) REVERT: X 5 LYS cc_start: 0.8200 (mmmm) cc_final: 0.7650 (mmtt) REVERT: X 6 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6824 (tm-30) REVERT: X 45 ARG cc_start: 0.8947 (mmt90) cc_final: 0.8732 (mtt-85) REVERT: X 49 GLN cc_start: 0.9292 (tm-30) cc_final: 0.8811 (tm-30) REVERT: X 64 GLU cc_start: 0.8614 (mp0) cc_final: 0.8133 (mp0) REVERT: X 69 GLN cc_start: 0.9002 (tm-30) cc_final: 0.8543 (tp-100) outliers start: 69 outliers final: 29 residues processed: 280 average time/residue: 1.6155 time to fit residues: 515.4390 Evaluate side-chains 243 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 208 time to evaluate : 3.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 331 ASP Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain L residue 309 THR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 191 LYS Chi-restraints excluded: chain O residue 248 THR Chi-restraints excluded: chain O residue 250 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 218 LEU Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain U residue 289 PHE Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 454 ASP Chi-restraints excluded: chain T residue 526 THR Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain W residue 40 ASP Chi-restraints excluded: chain W residue 63 CYS Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain X residue 21 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 294 optimal weight: 5.9990 chunk 34 optimal weight: 0.0060 chunk 174 optimal weight: 0.6980 chunk 223 optimal weight: 7.9990 chunk 172 optimal weight: 2.9990 chunk 257 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 chunk 304 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 chunk 185 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 638 GLN O 106 GLN P 112 HIS ** U 374 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 HIS S 11 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27527 Z= 0.183 Angle : 0.586 11.647 37474 Z= 0.302 Chirality : 0.038 0.197 4300 Planarity : 0.004 0.052 4432 Dihedral : 16.146 81.511 4219 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.81 % Allowed : 21.15 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 1.91 (0.16), residues: 3064 helix: 2.22 (0.12), residues: 1943 sheet: 0.56 (0.30), residues: 301 loop : -0.81 (0.21), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 718 HIS 0.020 0.001 HIS I 91 PHE 0.025 0.001 PHE O 287 TYR 0.020 0.001 TYR S 25 ARG 0.011 0.000 ARG U 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 230 time to evaluate : 3.099 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 135 PRO cc_start: 0.7441 (Cg_exo) cc_final: 0.6960 (Cg_endo) REVERT: I 171 MET cc_start: 0.8097 (OUTLIER) cc_final: 0.7642 (mtt) REVERT: I 268 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8084 (tt) REVERT: I 514 MET cc_start: 0.5968 (OUTLIER) cc_final: 0.5283 (mpp) REVERT: O 25 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7641 (tp30) REVERT: O 136 ASP cc_start: 0.8252 (OUTLIER) cc_final: 0.7923 (m-30) REVERT: P 247 LEU cc_start: 0.5000 (OUTLIER) cc_final: 0.4631 (tt) REVERT: Q 93 MET cc_start: 0.9105 (ttp) cc_final: 0.8635 (tmt) REVERT: Q 147 ARG cc_start: 0.8354 (ttm-80) cc_final: 0.8070 (mtp85) REVERT: U 406 ASN cc_start: 0.8742 (m110) cc_final: 0.8388 (m-40) REVERT: R 87 MET cc_start: 0.7619 (mpm) cc_final: 0.7108 (mmp) REVERT: R 104 MET cc_start: 0.7930 (tpt) cc_final: 0.7480 (ptt) REVERT: T 476 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7546 (mt-10) REVERT: S 38 LYS cc_start: 0.9038 (tppp) cc_final: 0.8529 (tttt) REVERT: S 67 MET cc_start: 0.8643 (ttp) cc_final: 0.8401 (ttm) REVERT: X 49 GLN cc_start: 0.9265 (tm-30) cc_final: 0.8695 (tm-30) REVERT: X 69 GLN cc_start: 0.8990 (tm-30) cc_final: 0.8512 (tp-100) outliers start: 51 outliers final: 25 residues processed: 264 average time/residue: 1.6631 time to fit residues: 497.5380 Evaluate side-chains 239 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 208 time to evaluate : 3.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 331 ASP Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 248 THR Chi-restraints excluded: chain O residue 250 VAL Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain R residue 127 CYS Chi-restraints excluded: chain R residue 131 PHE Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 454 ASP Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain W residue 7 VAL Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain X residue 64 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 188 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 193 optimal weight: 0.5980 chunk 207 optimal weight: 0.8980 chunk 150 optimal weight: 0.0050 chunk 28 optimal weight: 7.9990 chunk 239 optimal weight: 5.9990 chunk 277 optimal weight: 2.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 106 GLN P 112 HIS R 130 HIS S 11 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 27527 Z= 0.160 Angle : 0.582 12.482 37474 Z= 0.301 Chirality : 0.037 0.192 4300 Planarity : 0.004 0.054 4432 Dihedral : 16.013 81.442 4219 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.78 % Allowed : 21.40 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 2.06 (0.16), residues: 3064 helix: 2.29 (0.12), residues: 1944 sheet: 0.68 (0.30), residues: 302 loop : -0.68 (0.22), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 718 HIS 0.013 0.001 HIS P 112 PHE 0.027 0.001 PHE O 287 TYR 0.023 0.001 TYR I 72 ARG 0.016 0.000 ARG K 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 230 time to evaluate : 3.147 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: I 135 PRO cc_start: 0.7448 (Cg_exo) cc_final: 0.7025 (Cg_endo) REVERT: I 171 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7569 (mtt) REVERT: I 268 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8112 (tt) REVERT: I 514 MET cc_start: 0.5930 (OUTLIER) cc_final: 0.5213 (mpp) REVERT: O 25 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7579 (tp30) REVERT: O 136 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7903 (m-30) REVERT: P 247 LEU cc_start: 0.4863 (OUTLIER) cc_final: 0.4574 (tt) REVERT: Q 93 MET cc_start: 0.9082 (ttp) cc_final: 0.8653 (tmt) REVERT: Q 147 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.8081 (mtp85) REVERT: U 406 ASN cc_start: 0.8764 (m110) cc_final: 0.8401 (m-40) REVERT: R 87 MET cc_start: 0.7606 (mpm) cc_final: 0.7028 (mmp) REVERT: R 104 MET cc_start: 0.7888 (tpt) cc_final: 0.7495 (ptt) REVERT: R 131 PHE cc_start: 0.6569 (OUTLIER) cc_final: 0.6286 (p90) REVERT: R 134 ARG cc_start: 0.8780 (ppt90) cc_final: 0.8558 (pmt-80) REVERT: T 476 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7500 (mt-10) REVERT: S 38 LYS cc_start: 0.9074 (tppp) cc_final: 0.8576 (tttt) REVERT: S 67 MET cc_start: 0.8543 (ttp) cc_final: 0.8320 (ttm) REVERT: X 6 GLU cc_start: 0.7219 (tm-30) cc_final: 0.6944 (tm-30) REVERT: X 41 GLU cc_start: 0.8461 (mm-30) cc_final: 0.7419 (tp30) REVERT: X 45 ARG cc_start: 0.8699 (mmt90) cc_final: 0.8344 (mpt-90) REVERT: X 49 GLN cc_start: 0.9228 (tm-30) cc_final: 0.8664 (tm-30) REVERT: X 59 ASP cc_start: 0.7879 (OUTLIER) cc_final: 0.7552 (m-30) REVERT: X 69 GLN cc_start: 0.8833 (tm-30) cc_final: 0.8623 (tp-100) outliers start: 50 outliers final: 26 residues processed: 266 average time/residue: 1.6383 time to fit residues: 496.0489 Evaluate side-chains 251 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 217 time to evaluate : 3.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 331 ASP Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 99 GLU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 136 ASP Chi-restraints excluded: chain O residue 248 THR Chi-restraints excluded: chain O residue 250 VAL Chi-restraints excluded: chain O residue 257 VAL Chi-restraints excluded: chain O residue 266 GLU Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 247 LEU Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain R residue 131 PHE Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 454 ASP Chi-restraints excluded: chain T residue 526 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain W residue 7 VAL Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain X residue 59 ASP Chi-restraints excluded: chain X residue 64 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 291 optimal weight: 0.9990 chunk 266 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 123 optimal weight: 1.9990 chunk 222 optimal weight: 10.0000 chunk 87 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 268 optimal weight: 20.0000 chunk 282 optimal weight: 1.9990 chunk 186 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 HIS R 130 HIS X 29 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 27527 Z= 0.233 Angle : 0.615 12.348 37474 Z= 0.317 Chirality : 0.039 0.185 4300 Planarity : 0.004 0.052 4432 Dihedral : 16.004 81.035 4219 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.71 % Allowed : 21.65 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 2.01 (0.16), residues: 3064 helix: 2.23 (0.12), residues: 1946 sheet: 0.71 (0.30), residues: 296 loop : -0.64 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 718 HIS 0.010 0.001 HIS P 112 PHE 0.022 0.001 PHE O 287 TYR 0.027 0.001 TYR I 72 ARG 0.015 0.001 ARG X 48 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 219 time to evaluate : 3.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 133 MET cc_start: 0.7844 (mmt) cc_final: 0.7598 (mmp) REVERT: I 135 PRO cc_start: 0.7529 (Cg_exo) cc_final: 0.7069 (Cg_endo) REVERT: I 171 MET cc_start: 0.8064 (OUTLIER) cc_final: 0.7615 (mtt) REVERT: I 268 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8303 (mt) REVERT: I 514 MET cc_start: 0.5946 (OUTLIER) cc_final: 0.5603 (mtp) REVERT: O 25 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7655 (tp30) REVERT: Q 93 MET cc_start: 0.9108 (ttp) cc_final: 0.8537 (tmt) REVERT: Q 147 ARG cc_start: 0.8350 (ttm-80) cc_final: 0.8083 (mtp85) REVERT: U 406 ASN cc_start: 0.8745 (m110) cc_final: 0.8390 (m-40) REVERT: R 87 MET cc_start: 0.7414 (mpm) cc_final: 0.6903 (mmp) REVERT: R 104 MET cc_start: 0.7908 (tpt) cc_final: 0.7493 (ptt) REVERT: R 138 LYS cc_start: 0.8362 (ttpp) cc_final: 0.8104 (pttm) REVERT: T 476 GLU cc_start: 0.7839 (mt-10) cc_final: 0.7556 (mt-10) REVERT: S 38 LYS cc_start: 0.9079 (tppp) cc_final: 0.8590 (tttt) REVERT: X 49 GLN cc_start: 0.9240 (tm-30) cc_final: 0.8681 (tm-30) REVERT: X 59 ASP cc_start: 0.7897 (m-30) cc_final: 0.7564 (m-30) REVERT: X 69 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8582 (tp-100) outliers start: 48 outliers final: 30 residues processed: 254 average time/residue: 1.6174 time to fit residues: 468.7906 Evaluate side-chains 238 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 204 time to evaluate : 3.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 331 ASP Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain K residue 35 MET Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain L residue 309 THR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain N residue 128 GLU Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 99 GLU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 248 THR Chi-restraints excluded: chain O residue 250 VAL Chi-restraints excluded: chain O residue 266 GLU Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 454 ASP Chi-restraints excluded: chain T residue 526 THR Chi-restraints excluded: chain T residue 552 TYR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain W residue 7 VAL Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain X residue 64 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 300 optimal weight: 5.9990 chunk 183 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 208 optimal weight: 0.7980 chunk 314 optimal weight: 10.0000 chunk 289 optimal weight: 3.9990 chunk 250 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 193 optimal weight: 0.7980 chunk 153 optimal weight: 0.7980 chunk 199 optimal weight: 3.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 HIS Q 136 ASN R 130 HIS X 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 27527 Z= 0.208 Angle : 0.633 14.117 37474 Z= 0.324 Chirality : 0.039 0.201 4300 Planarity : 0.004 0.054 4432 Dihedral : 15.960 81.280 4219 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.24 % Allowed : 22.25 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 2.01 (0.16), residues: 3064 helix: 2.23 (0.12), residues: 1947 sheet: 0.64 (0.30), residues: 302 loop : -0.60 (0.22), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 718 HIS 0.018 0.001 HIS P 112 PHE 0.024 0.001 PHE R 86 TYR 0.030 0.001 TYR I 72 ARG 0.015 0.000 ARG X 48 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6128 Ramachandran restraints generated. 3064 Oldfield, 0 Emsley, 3064 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 214 time to evaluate : 3.225 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: I 133 MET cc_start: 0.7684 (mmt) cc_final: 0.7478 (mmp) REVERT: I 135 PRO cc_start: 0.7576 (Cg_exo) cc_final: 0.7123 (Cg_endo) REVERT: I 171 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7611 (mtt) REVERT: I 268 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8354 (mt) REVERT: I 514 MET cc_start: 0.5918 (OUTLIER) cc_final: 0.5397 (mtm) REVERT: O 25 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7651 (tp30) REVERT: P 112 HIS cc_start: 0.8066 (OUTLIER) cc_final: 0.7795 (t-170) REVERT: Q 93 MET cc_start: 0.9099 (ttp) cc_final: 0.8556 (tmt) REVERT: Q 147 ARG cc_start: 0.8348 (ttm-80) cc_final: 0.8092 (mtp85) REVERT: U 406 ASN cc_start: 0.8736 (m110) cc_final: 0.8389 (m-40) REVERT: R 87 MET cc_start: 0.7408 (mpm) cc_final: 0.6804 (mmp) REVERT: R 104 MET cc_start: 0.8007 (tpt) cc_final: 0.7532 (ptt) REVERT: R 138 LYS cc_start: 0.8376 (ttpp) cc_final: 0.8161 (pttm) REVERT: T 476 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7564 (mt-10) REVERT: S 6 GLU cc_start: 0.7587 (tp30) cc_final: 0.7176 (pp20) REVERT: S 38 LYS cc_start: 0.9079 (tppp) cc_final: 0.8576 (tttt) REVERT: S 101 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8765 (mm-30) REVERT: X 41 GLU cc_start: 0.8432 (mm-30) cc_final: 0.7782 (tp30) REVERT: X 45 ARG cc_start: 0.8763 (mmt90) cc_final: 0.8490 (mmt90) REVERT: X 48 ARG cc_start: 0.8103 (mtm110) cc_final: 0.7841 (mtm110) REVERT: X 49 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8686 (tm-30) REVERT: X 59 ASP cc_start: 0.7914 (OUTLIER) cc_final: 0.7592 (m-30) REVERT: X 69 GLN cc_start: 0.8836 (tm-30) cc_final: 0.8578 (tp-100) outliers start: 35 outliers final: 26 residues processed: 240 average time/residue: 1.6876 time to fit residues: 460.8675 Evaluate side-chains 237 residues out of total 2861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 205 time to evaluate : 3.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 38 ASP Chi-restraints excluded: chain I residue 171 MET Chi-restraints excluded: chain I residue 183 LEU Chi-restraints excluded: chain I residue 268 LEU Chi-restraints excluded: chain I residue 318 TYR Chi-restraints excluded: chain I residue 331 ASP Chi-restraints excluded: chain I residue 514 MET Chi-restraints excluded: chain I residue 583 PHE Chi-restraints excluded: chain K residue 260 THR Chi-restraints excluded: chain M residue 92 PHE Chi-restraints excluded: chain N residue 128 GLU Chi-restraints excluded: chain O residue 25 GLU Chi-restraints excluded: chain O residue 122 VAL Chi-restraints excluded: chain O residue 248 THR Chi-restraints excluded: chain O residue 250 VAL Chi-restraints excluded: chain O residue 266 GLU Chi-restraints excluded: chain O residue 278 LYS Chi-restraints excluded: chain P residue 60 LEU Chi-restraints excluded: chain P residue 112 HIS Chi-restraints excluded: chain P residue 179 TYR Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 255 ILE Chi-restraints excluded: chain Q residue 121 CYS Chi-restraints excluded: chain Q residue 253 SER Chi-restraints excluded: chain R residue 137 GLN Chi-restraints excluded: chain T residue 454 ASP Chi-restraints excluded: chain T residue 526 THR Chi-restraints excluded: chain T residue 557 VAL Chi-restraints excluded: chain W residue 7 VAL Chi-restraints excluded: chain S residue 90 ASN Chi-restraints excluded: chain X residue 59 ASP Chi-restraints excluded: chain X residue 64 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 316 random chunks: chunk 267 optimal weight: 9.9990 chunk 76 optimal weight: 0.8980 chunk 231 optimal weight: 0.1980 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 251 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 257 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 220 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 HIS R 130 HIS S 11 GLN X 29 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.083530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.050776 restraints weight = 87304.103| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 3.06 r_work: 0.2813 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 27527 Z= 0.175 Angle : 0.621 12.598 37474 Z= 0.319 Chirality : 0.038 0.208 4300 Planarity : 0.004 0.058 4432 Dihedral : 15.895 81.439 4219 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.42 % Allowed : 22.08 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.00 % 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: 2.09 (0.16), residues: 3064 helix: 2.29 (0.12), residues: 1945 sheet: 0.71 (0.31), residues: 302 loop : -0.57 (0.22), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 718 HIS 0.019 0.001 HIS P 112 PHE 0.026 0.001 PHE O 287 TYR 0.028 0.001 TYR I 72 ARG 0.014 0.000 ARG X 48 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9642.50 seconds wall clock time: 171 minutes 45.59 seconds (10305.59 seconds total)