Starting phenix.real_space_refine on Sun Mar 24 23:06:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gej_4395/03_2024/6gej_4395_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gej_4395/03_2024/6gej_4395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gej_4395/03_2024/6gej_4395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gej_4395/03_2024/6gej_4395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gej_4395/03_2024/6gej_4395_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gej_4395/03_2024/6gej_4395_updated.pdb" } resolution = 3.6 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= 0.001 sd= 0.008 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 966 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 324 5.49 5 Mg 8 5.21 5 S 118 5.16 5 Be 2 3.05 5 C 26529 2.51 5 N 7737 2.21 5 O 8976 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 36": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 36": "NH1" <-> "NH2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F ARG 36": "NH1" <-> "NH2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 72": "NH1" <-> "NH2" Residue "F ARG 82": "NH1" <-> "NH2" Residue "F ARG 89": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "H ARG 95": "NH1" <-> "NH2" Residue "M ARG 693": "NH1" <-> "NH2" Residue "M ARG 697": "NH1" <-> "NH2" Residue "M TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 766": "NH1" <-> "NH2" Residue "M PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 787": "NH1" <-> "NH2" Residue "M ARG 815": "NH1" <-> "NH2" Residue "M ARG 833": "NH1" <-> "NH2" Residue "M ARG 926": "NH1" <-> "NH2" Residue "M ARG 956": "NH1" <-> "NH2" Residue "M TYR 961": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 967": "NH1" <-> "NH2" Residue "M PHE 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 1023": "NH1" <-> "NH2" Residue "M PHE 1047": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 1057": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 1133": "NH1" <-> "NH2" Residue "M ASP 1178": "OD1" <-> "OD2" Residue "M ARG 1291": "NH1" <-> "NH2" Residue "M ARG 1313": "NH1" <-> "NH2" Residue "M ARG 1357": "NH1" <-> "NH2" Residue "M TYR 1367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 1369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 1387": "NH1" <-> "NH2" Residue "R PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 59": "NH1" <-> "NH2" Residue "R PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 221": "NH1" <-> "NH2" Residue "R ARG 234": "NH1" <-> "NH2" Residue "R PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 288": "NH1" <-> "NH2" Residue "R ARG 291": "NH1" <-> "NH2" Residue "R PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 194": "NH1" <-> "NH2" Residue "S TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 276": "NH1" <-> "NH2" Residue "T ARG 23": "NH1" <-> "NH2" Residue "T PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 126": "NH1" <-> "NH2" Residue "T TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 223": "OD1" <-> "OD2" Residue "T ARG 258": "NH1" <-> "NH2" Residue "T ARG 348": "NH1" <-> "NH2" Residue "T ASP 378": "OD1" <-> "OD2" Residue "T ARG 392": "NH1" <-> "NH2" Residue "U ARG 52": "NH1" <-> "NH2" Residue "U ARG 69": "NH1" <-> "NH2" Residue "U PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 122": "NH1" <-> "NH2" Residue "U TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 182": "OE1" <-> "OE2" Residue "U ARG 204": "NH1" <-> "NH2" Residue "U PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 266": "NH1" <-> "NH2" Residue "U ARG 333": "NH1" <-> "NH2" Residue "U ARG 397": "NH1" <-> "NH2" Residue "U ARG 413": "NH1" <-> "NH2" Residue "U ARG 425": "NH1" <-> "NH2" Residue "U ARG 435": "NH1" <-> "NH2" Residue "U TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 444": "OE1" <-> "OE2" Residue "V ARG 23": "NH1" <-> "NH2" Residue "V ARG 191": "NH1" <-> "NH2" Residue "V ASP 198": "OD1" <-> "OD2" Residue "V TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 242": "OE1" <-> "OE2" Residue "V ARG 258": "NH1" <-> "NH2" Residue "V ARG 348": "NH1" <-> "NH2" Residue "V ASP 365": "OD1" <-> "OD2" Residue "V ARG 392": "NH1" <-> "NH2" Residue "V ARG 413": "NH1" <-> "NH2" Residue "V TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 52": "NH1" <-> "NH2" Residue "W ARG 69": "NH1" <-> "NH2" Residue "W PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 122": "NH1" <-> "NH2" Residue "W TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 188": "OD1" <-> "OD2" Residue "W ARG 204": "NH1" <-> "NH2" Residue "W PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 228": "OE1" <-> "OE2" Residue "W PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 266": "NH1" <-> "NH2" Residue "W ARG 311": "NH1" <-> "NH2" Residue "W ARG 333": "NH1" <-> "NH2" Residue "W TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 397": "NH1" <-> "NH2" Residue "W ARG 413": "NH1" <-> "NH2" Residue "W GLU 421": "OE1" <-> "OE2" Residue "W ARG 425": "NH1" <-> "NH2" Residue "W ARG 435": "NH1" <-> "NH2" Residue "W TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 23": "NH1" <-> "NH2" Residue "X GLU 37": "OE1" <-> "OE2" Residue "X ARG 43": "NH1" <-> "NH2" Residue "X PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 126": "NH1" <-> "NH2" Residue "X ARG 132": "NH1" <-> "NH2" Residue "X TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 180": "NH1" <-> "NH2" Residue "X TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 191": "NH1" <-> "NH2" Residue "X ASP 198": "OD1" <-> "OD2" Residue "X TYR 201": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 214": "NH1" <-> "NH2" Residue "X TYR 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 221": "OE1" <-> "OE2" Residue "X TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 236": "OE1" <-> "OE2" Residue "X ARG 348": "NH1" <-> "NH2" Residue "X ASP 365": "OD1" <-> "OD2" Residue "X GLU 385": "OE1" <-> "OE2" Residue "X ARG 386": "NH1" <-> "NH2" Residue "X PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 33": "OE1" <-> "OE2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Y ARG 69": "NH1" <-> "NH2" Residue "Y PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 122": "NH1" <-> "NH2" Residue "Y TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 204": "NH1" <-> "NH2" Residue "Y PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 210": "NH1" <-> "NH2" Residue "Y ASP 218": "OD1" <-> "OD2" Residue "Y PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 311": "NH1" <-> "NH2" Residue "Y ASP 315": "OD1" <-> "OD2" Residue "Y ARG 333": "NH1" <-> "NH2" Residue "Y TYR 337": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 397": "NH1" <-> "NH2" Residue "Y ARG 413": "NH1" <-> "NH2" Residue "Y ARG 425": "NH1" <-> "NH2" Residue "Y ARG 435": "NH1" <-> "NH2" Residue "Y ASP 450": "OD1" <-> "OD2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 43702 Number of models: 1 Model: "" Number of chains: 29 Chain: "Z" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 655 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'TRANS': 130} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 131 Planarities with less than four sites: {'UNK:plan-1': 131} Unresolved non-hydrogen planarities: 131 Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 651 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "F" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 779 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "G" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 746 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "H" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 712 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 3137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3137 Classifications: {'DNA': 154} Link IDs: {'rna3p': 153} Chain: "J" Number of atoms: 3177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 3177 Classifications: {'DNA': 154} Link IDs: {'rna3p': 153} Chain: "M" Number of atoms: 5398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5398 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 19, 'TRANS': 668} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 167 Chain: "R" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3335 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 25, 'TRANS': 385} Chain breaks: 1 Chain: "S" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1695 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 10, 'TRANS': 197} Chain breaks: 3 Chain: "T" Number of atoms: 3391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3391 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 424} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3299 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 419} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3336 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "W" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3325 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 422} 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: "X" Number of atoms: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3397 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "Y" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3410 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 436} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23040 SG CYS S 244 89.133 119.821 106.290 1.00 89.97 S ATOM 23060 SG CYS S 247 92.310 121.520 103.015 1.00 92.50 S ATOM 23176 SG CYS S 264 91.902 118.182 103.872 1.00 91.58 S ATOM 23201 SG CYS S 268 93.891 120.081 106.264 1.00102.36 S ATOM 23120 SG CYS S 256 87.365 114.091 115.274 1.00 92.66 S ATOM 23141 SG CYS S 259 85.271 117.144 116.015 1.00 90.81 S ATOM 23280 SG CYS S 277 87.907 117.396 119.028 1.00103.89 S Time building chain proxies: 29.54, per 1000 atoms: 0.68 Number of scatterers: 43702 At special positions: 0 Unit cell: (147.63, 197.58, 203.13, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 118 16.00 P 324 15.00 Mg 8 11.99 F 6 9.00 O 8976 8.00 N 7737 7.00 C 26529 6.00 Be 2 4.00 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.58 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN S 501 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 264 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 247 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 244 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 268 " pdb=" ZN S 502 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 259 " pdb="ZN ZN S 502 " - pdb=" NE2 HIS S 272 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 277 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 256 " Number of angles added : 9 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9030 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 194 helices and 33 sheets defined 44.2% alpha, 11.0% beta 151 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 21.44 Creating SS restraints... Processing helix chain 'Z' and resid 102 through 128 Processing helix chain 'Z' and resid 137 through 143 Processing helix chain 'Z' and resid 199 through 206 Processing helix chain 'A' and resid 45 through 55 removed outlier: 3.660A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 89 through 113 Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.893A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 55 removed outlier: 3.660A pdb=" N ARG B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 64 through 76 Processing helix chain 'B' and resid 89 through 113 Processing helix chain 'B' and resid 121 through 131 removed outlier: 3.894A pdb=" N ARG B 131 " --> pdb=" O ALA B 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 28 No H-bonds generated for 'chain 'C' and resid 26 through 28' Processing helix chain 'C' and resid 31 through 40 Processing helix chain 'C' and resid 50 through 75 removed outlier: 3.578A pdb=" N GLU C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASP C 68 " --> pdb=" O SER C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 91 Processing helix chain 'D' and resid 26 through 28 No H-bonds generated for 'chain 'D' and resid 26 through 28' Processing helix chain 'D' and resid 31 through 40 Processing helix chain 'D' and resid 50 through 75 removed outlier: 3.578A pdb=" N GLU D 63 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ASP D 68 " --> pdb=" O SER D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 91 Processing helix chain 'E' and resid 18 through 21 No H-bonds generated for 'chain 'E' and resid 18 through 21' Processing helix chain 'E' and resid 28 through 37 Processing helix chain 'E' and resid 48 through 73 Processing helix chain 'E' and resid 81 through 90 Processing helix chain 'E' and resid 92 through 97 Processing helix chain 'F' and resid 18 through 21 No H-bonds generated for 'chain 'F' and resid 18 through 21' Processing helix chain 'F' and resid 28 through 37 Processing helix chain 'F' and resid 48 through 73 Processing helix chain 'F' and resid 81 through 90 Processing helix chain 'F' and resid 92 through 97 Processing helix chain 'G' and resid 41 through 51 Processing helix chain 'G' and resid 59 through 86 removed outlier: 3.511A pdb=" N GLU G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 94 through 104 Processing helix chain 'G' and resid 107 through 125 Processing helix chain 'H' and resid 41 through 51 Processing helix chain 'H' and resid 59 through 86 removed outlier: 3.510A pdb=" N GLU H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 107 through 124 Processing helix chain 'M' and resid 698 through 711 removed outlier: 4.163A pdb=" N SER M 709 " --> pdb=" O ASN M 705 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU M 710 " --> pdb=" O TRP M 706 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N TYR M 711 " --> pdb=" O LEU M 707 " (cutoff:3.500A) Processing helix chain 'M' and resid 727 through 741 removed outlier: 3.706A pdb=" N ALA M 739 " --> pdb=" O LEU M 735 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS M 740 " --> pdb=" O ALA M 736 " (cutoff:3.500A) Processing helix chain 'M' and resid 757 through 766 removed outlier: 3.919A pdb=" N GLU M 761 " --> pdb=" O LEU M 757 " (cutoff:3.500A) Processing helix chain 'M' and resid 782 through 787 Processing helix chain 'M' and resid 804 through 813 removed outlier: 3.960A pdb=" N ASP M 809 " --> pdb=" O VAL M 806 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLN M 810 " --> pdb=" O VAL M 807 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N HIS M 811 " --> pdb=" O GLN M 808 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE M 813 " --> pdb=" O GLN M 810 " (cutoff:3.500A) Processing helix chain 'M' and resid 835 through 839 Processing helix chain 'M' and resid 860 through 870 Processing helix chain 'M' and resid 914 through 924 removed outlier: 3.687A pdb=" N HIS M 922 " --> pdb=" O VAL M 918 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN M 923 " --> pdb=" O ALA M 919 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N VAL M 924 " --> pdb=" O LYS M 920 " (cutoff:3.500A) Processing helix chain 'M' and resid 955 through 970 Processing helix chain 'M' and resid 972 through 974 No H-bonds generated for 'chain 'M' and resid 972 through 974' Processing helix chain 'M' and resid 979 through 993 removed outlier: 3.683A pdb=" N VAL M 983 " --> pdb=" O PHE M 979 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N GLN M 988 " --> pdb=" O ASN M 984 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LEU M 989 " --> pdb=" O CYS M 985 " (cutoff:3.500A) Processing helix chain 'M' and resid 1014 through 1029 removed outlier: 3.597A pdb=" N TYR M1018 " --> pdb=" O VAL M1014 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ASP M1020 " --> pdb=" O SER M1016 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N VAL M1021 " --> pdb=" O ASP M1017 " (cutoff:3.500A) Processing helix chain 'M' and resid 1047 through 1049 No H-bonds generated for 'chain 'M' and resid 1047 through 1049' Processing helix chain 'M' and resid 1057 through 1064 Processing helix chain 'M' and resid 1070 through 1093 removed outlier: 3.585A pdb=" N LEU M1078 " --> pdb=" O GLU M1074 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU M1080 " --> pdb=" O ASN M1076 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N THR M1081 " --> pdb=" O LYS M1077 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU M1085 " --> pdb=" O THR M1081 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU M1088 " --> pdb=" O GLN M1084 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N GLU M1091 " --> pdb=" O GLU M1087 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N ALA M1092 " --> pdb=" O GLU M1088 " (cutoff:3.500A) Processing helix chain 'M' and resid 1104 through 1133 removed outlier: 3.623A pdb=" N ASN M1108 " --> pdb=" O PHE M1104 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ASP M1117 " --> pdb=" O GLU M1113 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N MET M1118 " --> pdb=" O GLY M1114 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU M1122 " --> pdb=" O MET M1118 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LYS M1123 " --> pdb=" O LEU M1119 " (cutoff:3.500A) Processing helix chain 'M' and resid 1142 through 1146 Processing helix chain 'M' and resid 1158 through 1163 removed outlier: 3.787A pdb=" N ILE M1163 " --> pdb=" O ASN M1160 " (cutoff:3.500A) Processing helix chain 'M' and resid 1166 through 1172 removed outlier: 3.800A pdb=" N LEU M1171 " --> pdb=" O GLN M1167 " (cutoff:3.500A) Processing helix chain 'M' and resid 1174 through 1180 Processing helix chain 'M' and resid 1192 through 1197 Processing helix chain 'M' and resid 1207 through 1219 removed outlier: 3.794A pdb=" N LEU M1211 " --> pdb=" O GLU M1207 " (cutoff:3.500A) Processing helix chain 'M' and resid 1223 through 1232 removed outlier: 4.175A pdb=" N GLN M1226 " --> pdb=" O PRO M1223 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS M1230 " --> pdb=" O LEU M1227 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR M1232 " --> pdb=" O THR M1229 " (cutoff:3.500A) Processing helix chain 'M' and resid 1240 through 1243 No H-bonds generated for 'chain 'M' and resid 1240 through 1243' Processing helix chain 'M' and resid 1251 through 1260 Processing helix chain 'M' and resid 1272 through 1285 removed outlier: 4.305A pdb=" N ASP M1276 " --> pdb=" O LYS M1273 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU M1282 " --> pdb=" O GLU M1279 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ASN M1283 " --> pdb=" O GLN M1280 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N HIS M1285 " --> pdb=" O LEU M1282 " (cutoff:3.500A) Processing helix chain 'M' and resid 1299 through 1309 removed outlier: 4.019A pdb=" N ILE M1303 " --> pdb=" O GLU M1299 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE M1308 " --> pdb=" O LEU M1304 " (cutoff:3.500A) Processing helix chain 'M' and resid 1349 through 1355 removed outlier: 3.832A pdb=" N CYS M1355 " --> pdb=" O CYS M1351 " (cutoff:3.500A) Processing helix chain 'M' and resid 1375 through 1385 removed outlier: 3.656A pdb=" N LEU M1380 " --> pdb=" O GLU M1376 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS M1381 " --> pdb=" O SER M1377 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLN M1385 " --> pdb=" O LYS M1381 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 48 No H-bonds generated for 'chain 'R' and resid 46 through 48' Processing helix chain 'R' and resid 69 through 81 Processing helix chain 'R' and resid 109 through 121 Processing helix chain 'R' and resid 133 through 142 removed outlier: 3.654A pdb=" N VAL R 137 " --> pdb=" O VAL R 133 " (cutoff:3.500A) Proline residue: R 138 - end of helix removed outlier: 4.980A pdb=" N LYS R 141 " --> pdb=" O VAL R 137 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N SER R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 133 through 142' Processing helix chain 'R' and resid 220 through 234 Processing helix chain 'R' and resid 242 through 252 Processing helix chain 'R' and resid 260 through 265 Processing helix chain 'R' and resid 308 through 316 Proline residue: R 314 - end of helix Processing helix chain 'R' and resid 320 through 323 Processing helix chain 'R' and resid 330 through 339 Processing helix chain 'R' and resid 343 through 349 Proline residue: R 347 - end of helix No H-bonds generated for 'chain 'R' and resid 343 through 349' Processing helix chain 'R' and resid 359 through 361 No H-bonds generated for 'chain 'R' and resid 359 through 361' Processing helix chain 'R' and resid 365 through 376 removed outlier: 3.854A pdb=" N GLN R 376 " --> pdb=" O GLU R 372 " (cutoff:3.500A) Processing helix chain 'R' and resid 392 through 405 removed outlier: 3.896A pdb=" N ALA R 404 " --> pdb=" O MET R 400 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS R 405 " --> pdb=" O SER R 401 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 412 removed outlier: 3.995A pdb=" N LYS R 411 " --> pdb=" O ASP R 407 " (cutoff:3.500A) Processing helix chain 'R' and resid 416 through 421 Processing helix chain 'R' and resid 424 through 429 removed outlier: 3.970A pdb=" N THR R 428 " --> pdb=" O PRO R 424 " (cutoff:3.500A) Processing helix chain 'S' and resid 53 through 60 Processing helix chain 'S' and resid 92 through 106 Processing helix chain 'S' and resid 113 through 124 Proline residue: S 117 - end of helix Processing helix chain 'S' and resid 128 through 134 Processing helix chain 'S' and resid 169 through 181 removed outlier: 4.495A pdb=" N SER S 181 " --> pdb=" O LEU S 177 " (cutoff:3.500A) Processing helix chain 'S' and resid 193 through 202 Processing helix chain 'S' and resid 208 through 213 Processing helix chain 'S' and resid 219 through 225 Processing helix chain 'S' and resid 266 through 272 Processing helix chain 'T' and resid 52 through 67 removed outlier: 3.522A pdb=" N VAL T 60 " --> pdb=" O GLU T 56 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE T 61 " --> pdb=" O ALA T 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 85 through 96 removed outlier: 3.781A pdb=" N SER T 93 " --> pdb=" O ALA T 89 " (cutoff:3.500A) Processing helix chain 'T' and resid 107 through 109 No H-bonds generated for 'chain 'T' and resid 107 through 109' Processing helix chain 'T' and resid 117 through 128 Processing helix chain 'T' and resid 183 through 192 Processing helix chain 'T' and resid 217 through 221 removed outlier: 3.994A pdb=" N THR T 220 " --> pdb=" O ALA T 217 " (cutoff:3.500A) Processing helix chain 'T' and resid 249 through 257 Processing helix chain 'T' and resid 265 through 272 Processing helix chain 'T' and resid 282 through 298 removed outlier: 3.555A pdb=" N ASP T 297 " --> pdb=" O ALA T 293 " (cutoff:3.500A) Processing helix chain 'T' and resid 313 through 315 No H-bonds generated for 'chain 'T' and resid 313 through 315' Processing helix chain 'T' and resid 318 through 328 removed outlier: 3.640A pdb=" N ASN T 325 " --> pdb=" O PHE T 321 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS T 326 " --> pdb=" O THR T 322 " (cutoff:3.500A) Processing helix chain 'T' and resid 356 through 358 No H-bonds generated for 'chain 'T' and resid 356 through 358' Processing helix chain 'T' and resid 361 through 366 removed outlier: 3.724A pdb=" N ARG T 366 " --> pdb=" O ASP T 362 " (cutoff:3.500A) Processing helix chain 'T' and resid 377 through 391 Processing helix chain 'T' and resid 397 through 409 removed outlier: 3.602A pdb=" N LEU T 402 " --> pdb=" O SER T 398 " (cutoff:3.500A) Processing helix chain 'T' and resid 412 through 428 removed outlier: 3.713A pdb=" N LEU T 416 " --> pdb=" O LEU T 412 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA T 420 " --> pdb=" O LEU T 416 " (cutoff:3.500A) Proline residue: T 421 - end of helix removed outlier: 4.192A pdb=" N ILE T 424 " --> pdb=" O ALA T 420 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 445 removed outlier: 3.974A pdb=" N LEU T 444 " --> pdb=" O ASN T 440 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU T 445 " --> pdb=" O GLU T 441 " (cutoff:3.500A) Processing helix chain 'T' and resid 449 through 457 Processing helix chain 'U' and resid 48 through 63 Processing helix chain 'U' and resid 82 through 92 Processing helix chain 'U' and resid 113 through 123 removed outlier: 3.800A pdb=" N ALA U 120 " --> pdb=" O ALA U 116 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE U 121 " --> pdb=" O LEU U 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 174 through 181 Processing helix chain 'U' and resid 241 through 249 removed outlier: 3.694A pdb=" N ILE U 247 " --> pdb=" O GLU U 243 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN U 248 " --> pdb=" O ILE U 244 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER U 249 " --> pdb=" O ASP U 245 " (cutoff:3.500A) Processing helix chain 'U' and resid 254 through 259 removed outlier: 3.556A pdb=" N PHE U 258 " --> pdb=" O PHE U 254 " (cutoff:3.500A) Processing helix chain 'U' and resid 267 through 283 removed outlier: 3.722A pdb=" N THR U 275 " --> pdb=" O ASP U 271 " (cutoff:3.500A) Processing helix chain 'U' and resid 298 through 300 No H-bonds generated for 'chain 'U' and resid 298 through 300' Processing helix chain 'U' and resid 303 through 313 removed outlier: 3.618A pdb=" N ASN U 310 " --> pdb=" O PHE U 306 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N ARG U 311 " --> pdb=" O SER U 307 " (cutoff:3.500A) Processing helix chain 'U' and resid 340 through 342 No H-bonds generated for 'chain 'U' and resid 340 through 342' Processing helix chain 'U' and resid 345 through 350 removed outlier: 3.823A pdb=" N ARG U 350 " --> pdb=" O ASP U 346 " (cutoff:3.500A) Processing helix chain 'U' and resid 361 through 374 removed outlier: 3.694A pdb=" N LYS U 365 " --> pdb=" O GLU U 361 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR U 366 " --> pdb=" O GLN U 362 " (cutoff:3.500A) Processing helix chain 'U' and resid 381 through 393 Processing helix chain 'U' and resid 396 through 412 removed outlier: 4.361A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL U 405 " --> pdb=" O ASN U 401 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLN U 407 " --> pdb=" O ILE U 403 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE U 409 " --> pdb=" O VAL U 405 " (cutoff:3.500A) Processing helix chain 'U' and resid 420 through 429 Processing helix chain 'U' and resid 433 through 443 removed outlier: 3.642A pdb=" N GLU U 442 " --> pdb=" O LYS U 438 " (cutoff:3.500A) Processing helix chain 'V' and resid 52 through 67 Processing helix chain 'V' and resid 85 through 96 removed outlier: 3.591A pdb=" N ALA V 91 " --> pdb=" O ALA V 87 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER V 93 " --> pdb=" O ALA V 89 " (cutoff:3.500A) Processing helix chain 'V' and resid 107 through 110 removed outlier: 3.666A pdb=" N LEU V 110 " --> pdb=" O GLY V 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 107 through 110' Processing helix chain 'V' and resid 117 through 127 removed outlier: 3.742A pdb=" N ASN V 124 " --> pdb=" O THR V 120 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N PHE V 125 " --> pdb=" O LEU V 121 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ARG V 126 " --> pdb=" O MET V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 183 through 192 Processing helix chain 'V' and resid 216 through 218 No H-bonds generated for 'chain 'V' and resid 216 through 218' Processing helix chain 'V' and resid 249 through 257 removed outlier: 3.581A pdb=" N ALA V 255 " --> pdb=" O ASP V 251 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN V 256 " --> pdb=" O LEU V 252 " (cutoff:3.500A) Processing helix chain 'V' and resid 265 through 273 Processing helix chain 'V' and resid 282 through 297 Processing helix chain 'V' and resid 313 through 315 No H-bonds generated for 'chain 'V' and resid 313 through 315' Processing helix chain 'V' and resid 318 through 327 removed outlier: 3.738A pdb=" N LYS V 326 " --> pdb=" O THR V 322 " (cutoff:3.500A) Processing helix chain 'V' and resid 356 through 358 No H-bonds generated for 'chain 'V' and resid 356 through 358' Processing helix chain 'V' and resid 361 through 365 removed outlier: 3.690A pdb=" N ASP V 365 " --> pdb=" O PRO V 361 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 361 through 365' Processing helix chain 'V' and resid 377 through 390 Processing helix chain 'V' and resid 397 through 409 Processing helix chain 'V' and resid 412 through 428 removed outlier: 3.821A pdb=" N LEU V 419 " --> pdb=" O ALA V 415 " (cutoff:3.500A) removed outlier: 5.096A pdb=" N ALA V 420 " --> pdb=" O LEU V 416 " (cutoff:3.500A) Proline residue: V 421 - end of helix Processing helix chain 'V' and resid 436 through 445 Processing helix chain 'V' and resid 449 through 457 Processing helix chain 'W' and resid 48 through 63 removed outlier: 3.517A pdb=" N ILE W 57 " --> pdb=" O ALA W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 81 through 92 Processing helix chain 'W' and resid 113 through 124 removed outlier: 3.974A pdb=" N SER W 124 " --> pdb=" O ALA W 120 " (cutoff:3.500A) Processing helix chain 'W' and resid 173 through 181 removed outlier: 3.862A pdb=" N ASP W 177 " --> pdb=" O ASN W 173 " (cutoff:3.500A) Processing helix chain 'W' and resid 241 through 247 Processing helix chain 'W' and resid 252 through 259 removed outlier: 4.100A pdb=" N THR W 259 " --> pdb=" O ALA W 256 " (cutoff:3.500A) Processing helix chain 'W' and resid 267 through 283 removed outlier: 3.525A pdb=" N THR W 275 " --> pdb=" O ASP W 271 " (cutoff:3.500A) Processing helix chain 'W' and resid 303 through 314 removed outlier: 3.872A pdb=" N ARG W 311 " --> pdb=" O SER W 307 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLU W 314 " --> pdb=" O ASN W 310 " (cutoff:3.500A) Processing helix chain 'W' and resid 340 through 342 No H-bonds generated for 'chain 'W' and resid 340 through 342' Processing helix chain 'W' and resid 345 through 350 removed outlier: 3.992A pdb=" N ARG W 350 " --> pdb=" O ASP W 346 " (cutoff:3.500A) Processing helix chain 'W' and resid 361 through 375 removed outlier: 3.508A pdb=" N LYS W 365 " --> pdb=" O GLU W 361 " (cutoff:3.500A) Processing helix chain 'W' and resid 381 through 393 Processing helix chain 'W' and resid 396 through 411 removed outlier: 3.585A pdb=" N ILE W 403 " --> pdb=" O SER W 399 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL W 405 " --> pdb=" O ASN W 401 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLN W 407 " --> pdb=" O ILE W 403 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLN W 408 " --> pdb=" O SER W 404 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 429 Processing helix chain 'W' and resid 433 through 442 removed outlier: 3.712A pdb=" N LYS W 438 " --> pdb=" O ALA W 434 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR W 439 " --> pdb=" O ARG W 435 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 67 Processing helix chain 'X' and resid 85 through 96 removed outlier: 3.736A pdb=" N ALA X 89 " --> pdb=" O LYS X 85 " (cutoff:3.500A) Processing helix chain 'X' and resid 107 through 110 removed outlier: 3.558A pdb=" N LEU X 110 " --> pdb=" O GLY X 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 107 through 110' Processing helix chain 'X' and resid 117 through 126 Processing helix chain 'X' and resid 183 through 192 removed outlier: 3.592A pdb=" N GLU X 187 " --> pdb=" O THR X 184 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE X 189 " --> pdb=" O TYR X 186 " (cutoff:3.500A) Processing helix chain 'X' and resid 216 through 218 No H-bonds generated for 'chain 'X' and resid 216 through 218' Processing helix chain 'X' and resid 249 through 257 removed outlier: 3.582A pdb=" N ALA X 255 " --> pdb=" O ASP X 251 " (cutoff:3.500A) Processing helix chain 'X' and resid 265 through 270 Processing helix chain 'X' and resid 282 through 297 Processing helix chain 'X' and resid 313 through 315 No H-bonds generated for 'chain 'X' and resid 313 through 315' Processing helix chain 'X' and resid 318 through 327 removed outlier: 3.575A pdb=" N ASN X 325 " --> pdb=" O PHE X 321 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS X 326 " --> pdb=" O THR X 322 " (cutoff:3.500A) Processing helix chain 'X' and resid 356 through 358 No H-bonds generated for 'chain 'X' and resid 356 through 358' Processing helix chain 'X' and resid 361 through 366 removed outlier: 3.951A pdb=" N ARG X 366 " --> pdb=" O ASP X 362 " (cutoff:3.500A) Processing helix chain 'X' and resid 377 through 391 removed outlier: 3.848A pdb=" N THR X 389 " --> pdb=" O GLU X 385 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL X 390 " --> pdb=" O ARG X 386 " (cutoff:3.500A) Processing helix chain 'X' and resid 398 through 409 removed outlier: 3.686A pdb=" N LEU X 402 " --> pdb=" O SER X 398 " (cutoff:3.500A) Processing helix chain 'X' and resid 412 through 428 removed outlier: 3.745A pdb=" N LEU X 419 " --> pdb=" O ALA X 415 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ALA X 420 " --> pdb=" O LEU X 416 " (cutoff:3.500A) Proline residue: X 421 - end of helix Processing helix chain 'X' and resid 436 through 445 Processing helix chain 'X' and resid 449 through 457 removed outlier: 3.772A pdb=" N GLU X 457 " --> pdb=" O THR X 453 " (cutoff:3.500A) Processing helix chain 'Y' and resid 48 through 63 removed outlier: 3.674A pdb=" N ILE Y 57 " --> pdb=" O ALA Y 53 " (cutoff:3.500A) Processing helix chain 'Y' and resid 82 through 92 Processing helix chain 'Y' and resid 103 through 106 removed outlier: 3.738A pdb=" N ILE Y 106 " --> pdb=" O GLY Y 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 103 through 106' Processing helix chain 'Y' and resid 113 through 122 Processing helix chain 'Y' and resid 173 through 180 Processing helix chain 'Y' and resid 206 through 208 No H-bonds generated for 'chain 'Y' and resid 206 through 208' Processing helix chain 'Y' and resid 241 through 249 Processing helix chain 'Y' and resid 254 through 259 Processing helix chain 'Y' and resid 267 through 283 removed outlier: 3.838A pdb=" N ASP Y 271 " --> pdb=" O SER Y 267 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN Y 272 " --> pdb=" O GLU Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 303 through 314 removed outlier: 4.702A pdb=" N GLU Y 314 " --> pdb=" O ASN Y 310 " (cutoff:3.500A) Processing helix chain 'Y' and resid 340 through 342 No H-bonds generated for 'chain 'Y' and resid 340 through 342' Processing helix chain 'Y' and resid 345 through 349 Processing helix chain 'Y' and resid 361 through 375 removed outlier: 3.519A pdb=" N LYS Y 365 " --> pdb=" O GLU Y 361 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR Y 366 " --> pdb=" O GLN Y 362 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU Y 374 " --> pdb=" O ILE Y 370 " (cutoff:3.500A) Processing helix chain 'Y' and resid 383 through 393 removed outlier: 3.627A pdb=" N GLU Y 393 " --> pdb=" O LYS Y 389 " (cutoff:3.500A) Processing helix chain 'Y' and resid 396 through 413 removed outlier: 3.916A pdb=" N SER Y 400 " --> pdb=" O LEU Y 396 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ASN Y 401 " --> pdb=" O ARG Y 397 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU Y 402 " --> pdb=" O TYR Y 398 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLN Y 407 " --> pdb=" O ILE Y 403 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG Y 413 " --> pdb=" O ILE Y 409 " (cutoff:3.500A) Processing helix chain 'Y' and resid 420 through 429 Processing helix chain 'Y' and resid 433 through 442 removed outlier: 3.757A pdb=" N VAL Y 437 " --> pdb=" O SER Y 433 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS Y 438 " --> pdb=" O ALA Y 434 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'Z' and resid 169 through 171 Processing sheet with id= B, first strand: chain 'M' and resid 719 through 721 removed outlier: 5.480A pdb=" N LEU M 930 " --> pdb=" O ALA M 720 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'M' and resid 800 through 802 removed outlier: 5.882A pdb=" N ILE M 750 " --> pdb=" O VAL M 801 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N ARG M 847 " --> pdb=" O MET M 821 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N LEU M 823 " --> pdb=" O ARG M 847 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N LEU M 849 " --> pdb=" O LEU M 823 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'M' and resid 944 through 946 removed outlier: 6.738A pdb=" N VAL M1364 " --> pdb=" O TYR M 945 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'M' and resid 949 through 951 Processing sheet with id= F, first strand: chain 'M' and resid 1335 through 1338 removed outlier: 4.077A pdb=" N THR M1269 " --> pdb=" O LEU M1319 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N MET M1290 " --> pdb=" O VAL M1316 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'R' and resid 127 through 130 removed outlier: 6.397A pdb=" N ILE R 6 " --> pdb=" O VAL R 100 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N SER R 102 " --> pdb=" O ILE R 6 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N ILE R 8 " --> pdb=" O SER R 102 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'R' and resid 32 through 35 Processing sheet with id= I, first strand: chain 'R' and resid 147 through 151 Processing sheet with id= J, first strand: chain 'R' and resid 353 through 356 removed outlier: 6.431A pdb=" N LEU R 189 " --> pdb=" O VAL R 354 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N THR R 356 " --> pdb=" O LEU R 189 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ILE R 191 " --> pdb=" O THR R 356 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'R' and resid 286 through 289 removed outlier: 3.976A pdb=" N TYR R 286 " --> pdb=" O VAL R 275 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL R 275 " --> pdb=" O TYR R 286 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'T' and resid 369 through 372 removed outlier: 8.558A pdb=" N VAL T 370 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU T 76 " --> pdb=" O VAL T 370 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR T 372 " --> pdb=" O LEU T 76 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ALA T 78 " --> pdb=" O THR T 372 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL T 336 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 7.975A pdb=" N LEU T 77 " --> pdb=" O VAL T 336 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU T 338 " --> pdb=" O LEU T 77 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N GLY T 79 " --> pdb=" O LEU T 338 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N SER T 340 " --> pdb=" O GLY T 79 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA T 339 " --> pdb=" O ILE T 310 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'T' and resid 246 through 248 Processing sheet with id= N, first strand: chain 'T' and resid 238 through 243 removed outlier: 3.713A pdb=" N GLY T 213 " --> pdb=" O VAL T 199 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR T 201 " --> pdb=" O ARG T 211 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N ARG T 211 " --> pdb=" O TYR T 201 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N GLU T 203 " --> pdb=" O VAL T 209 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL T 209 " --> pdb=" O GLU T 203 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'T' and resid 147 through 150 removed outlier: 3.593A pdb=" N HIS T 165 " --> pdb=" O GLU T 150 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'U' and resid 351 through 355 removed outlier: 7.208A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N VAL U 321 " --> pdb=" O VAL U 71 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N VAL U 73 " --> pdb=" O VAL U 321 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N MET U 323 " --> pdb=" O VAL U 73 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA U 324 " --> pdb=" O ILE U 295 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'U' and resid 286 through 290 removed outlier: 3.605A pdb=" N GLY U 126 " --> pdb=" O VAL U 289 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'U' and resid 166 through 170 removed outlier: 3.567A pdb=" N THR U 167 " --> pdb=" O ILE U 160 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU U 142 " --> pdb=" O THR U 159 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N LYS U 161 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL U 140 " --> pdb=" O LYS U 161 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL U 140 " --> pdb=" O ASP U 188 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASP U 188 " --> pdb=" O VAL U 140 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER U 191 " --> pdb=" O LYS U 201 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N LYS U 201 " --> pdb=" O SER U 191 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ASP U 193 " --> pdb=" O ILE U 199 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE U 199 " --> pdb=" O ASP U 193 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'V' and resid 367 through 371 removed outlier: 7.130A pdb=" N ALA V 74 " --> pdb=" O LEU V 368 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N VAL V 370 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LEU V 76 " --> pdb=" O VAL V 370 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VAL V 336 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N LEU V 77 " --> pdb=" O VAL V 336 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LEU V 338 " --> pdb=" O LEU V 77 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'V' and resid 246 through 248 removed outlier: 3.536A pdb=" N LEU V 131 " --> pdb=" O VAL V 247 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG V 132 " --> pdb=" O GLU V 302 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'V' and resid 238 through 243 removed outlier: 3.740A pdb=" N LYS V 241 " --> pdb=" O LYS V 137 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY V 142 " --> pdb=" O ILE V 200 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE V 200 " --> pdb=" O GLY V 142 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N TYR V 201 " --> pdb=" O ARG V 211 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG V 211 " --> pdb=" O TYR V 201 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N GLU V 203 " --> pdb=" O VAL V 209 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL V 209 " --> pdb=" O GLU V 203 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'V' and resid 147 through 149 removed outlier: 3.825A pdb=" N THR V 148 " --> pdb=" O ILE V 167 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE V 167 " --> pdb=" O THR V 148 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N VAL V 166 " --> pdb=" O LEU V 181 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'V' and resid 344 through 346 Processing sheet with id= X, first strand: chain 'W' and resid 351 through 354 removed outlier: 7.304A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N VAL W 321 " --> pdb=" O VAL W 71 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N VAL W 73 " --> pdb=" O VAL W 321 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N MET W 323 " --> pdb=" O VAL W 73 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'W' and resid 230 through 240 Processing sheet with id= Z, first strand: chain 'W' and resid 166 through 171 removed outlier: 4.273A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLU W 142 " --> pdb=" O THR W 159 " (cutoff:3.500A) removed outlier: 5.876A pdb=" N LYS W 161 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N VAL W 140 " --> pdb=" O LYS W 161 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ILE W 190 " --> pdb=" O GLY W 138 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL W 140 " --> pdb=" O ASP W 188 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N ASP W 188 " --> pdb=" O VAL W 140 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL W 189 " --> pdb=" O GLY W 203 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLY W 203 " --> pdb=" O VAL W 189 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N SER W 191 " --> pdb=" O LYS W 201 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LYS W 201 " --> pdb=" O SER W 191 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N ASP W 193 " --> pdb=" O ILE W 199 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE W 199 " --> pdb=" O ASP W 193 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'X' and resid 367 through 371 removed outlier: 7.568A pdb=" N ALA X 74 " --> pdb=" O LEU X 368 " (cutoff:3.500A) removed outlier: 8.670A pdb=" N VAL X 370 " --> pdb=" O ALA X 74 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU X 76 " --> pdb=" O VAL X 370 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL X 336 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N LEU X 77 " --> pdb=" O VAL X 336 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N LEU X 338 " --> pdb=" O LEU X 77 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA X 339 " --> pdb=" O ILE X 310 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'X' and resid 238 through 248 removed outlier: 3.706A pdb=" N LYS X 241 " --> pdb=" O LYS X 137 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'X' and resid 139 through 142 removed outlier: 3.912A pdb=" N GLY X 142 " --> pdb=" O ILE X 200 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY X 213 " --> pdb=" O VAL X 199 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR X 201 " --> pdb=" O ARG X 211 " (cutoff:3.500A) removed outlier: 5.379A pdb=" N ARG X 211 " --> pdb=" O TYR X 201 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'X' and resid 175 through 182 removed outlier: 7.010A pdb=" N GLU X 150 " --> pdb=" O SER X 164 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N VAL X 166 " --> pdb=" O THR X 148 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N THR X 148 " --> pdb=" O VAL X 166 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Y' and resid 353 through 355 removed outlier: 8.530A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL Y 321 " --> pdb=" O VAL Y 71 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL Y 73 " --> pdb=" O VAL Y 321 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N MET Y 323 " --> pdb=" O VAL Y 73 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA Y 324 " --> pdb=" O ILE Y 295 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Y' and resid 230 through 240 removed outlier: 3.625A pdb=" N LEU Y 135 " --> pdb=" O LYS Y 231 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'Y' and resid 166 through 170 removed outlier: 3.844A pdb=" N GLU Y 142 " --> pdb=" O THR Y 159 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N LYS Y 161 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N VAL Y 140 " --> pdb=" O LYS Y 161 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP Y 188 " --> pdb=" O VAL Y 140 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER Y 191 " --> pdb=" O LYS Y 201 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N LYS Y 201 " --> pdb=" O SER Y 191 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASP Y 193 " --> pdb=" O ILE Y 199 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ILE Y 199 " --> pdb=" O ASP Y 193 " (cutoff:3.500A) 1390 hydrogen bonds defined for protein. 4020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 383 hydrogen bonds 738 hydrogen bond angles 0 basepair planarities 151 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 26.98 Time building geometry restraints manager: 19.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12690 1.34 - 1.46: 7653 1.46 - 1.57: 23823 1.57 - 1.69: 638 1.69 - 1.81: 194 Bond restraints: 44998 Sorted by residual: bond pdb=" BE BEF R 502 " pdb=" F2 BEF R 502 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" BE BEF M1602 " pdb=" F2 BEF M1602 " ideal model delta sigma weight residual 1.476 1.562 -0.086 2.00e-02 2.50e+03 1.84e+01 bond pdb=" BE BEF M1602 " pdb=" F3 BEF M1602 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" BE BEF R 502 " pdb=" F3 BEF R 502 " ideal model delta sigma weight residual 1.476 1.546 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" BE BEF M1602 " pdb=" F1 BEF M1602 " ideal model delta sigma weight residual 1.476 1.535 -0.059 2.00e-02 2.50e+03 8.56e+00 ... (remaining 44993 not shown) Histogram of bond angle deviations from ideal: 97.54 - 105.30: 1878 105.30 - 113.06: 25796 113.06 - 120.82: 21168 120.82 - 128.59: 12975 128.59 - 136.35: 390 Bond angle restraints: 62207 Sorted by residual: angle pdb=" C LEU M 998 " pdb=" N PHE M 999 " pdb=" CA PHE M 999 " ideal model delta sigma weight residual 121.54 130.89 -9.35 1.91e+00 2.74e-01 2.39e+01 angle pdb=" N MET V 406 " pdb=" CA MET V 406 " pdb=" C MET V 406 " ideal model delta sigma weight residual 110.97 105.70 5.27 1.09e+00 8.42e-01 2.34e+01 angle pdb=" C LEU U 29 " pdb=" CA LEU U 29 " pdb=" CB LEU U 29 " ideal model delta sigma weight residual 116.54 111.05 5.49 1.15e+00 7.56e-01 2.28e+01 angle pdb=" F2 BEF M1602 " pdb=" BE BEF M1602 " pdb=" F3 BEF M1602 " ideal model delta sigma weight residual 119.96 107.15 12.81 3.00e+00 1.11e-01 1.82e+01 angle pdb=" F2 BEF R 502 " pdb=" BE BEF R 502 " pdb=" F3 BEF R 502 " ideal model delta sigma weight residual 119.96 107.27 12.69 3.00e+00 1.11e-01 1.79e+01 ... (remaining 62202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 24967 35.89 - 71.79: 1595 71.79 - 107.68: 34 107.68 - 143.57: 9 143.57 - 179.46: 4 Dihedral angle restraints: 26609 sinusoidal: 12658 harmonic: 13951 Sorted by residual: dihedral pdb=" CA UNK Z 188 " pdb=" C UNK Z 188 " pdb=" N UNK Z 189 " pdb=" CA UNK Z 189 " ideal model delta harmonic sigma weight residual -180.00 -139.72 -40.28 0 5.00e+00 4.00e-02 6.49e+01 dihedral pdb=" CA LEU M 692 " pdb=" C LEU M 692 " pdb=" N ARG M 693 " pdb=" CA ARG M 693 " ideal model delta harmonic sigma weight residual 180.00 -143.52 -36.48 0 5.00e+00 4.00e-02 5.32e+01 dihedral pdb=" C5' ADP W 501 " pdb=" O5' ADP W 501 " pdb=" PA ADP W 501 " pdb=" O2A ADP W 501 " ideal model delta sinusoidal sigma weight residual -60.00 119.47 -179.46 1 2.00e+01 2.50e-03 4.80e+01 ... (remaining 26606 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 5406 0.035 - 0.069: 1316 0.069 - 0.104: 406 0.104 - 0.139: 158 0.139 - 0.173: 2 Chirality restraints: 7288 Sorted by residual: chirality pdb=" CA MET V 406 " pdb=" N MET V 406 " pdb=" C MET V 406 " pdb=" CB MET V 406 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" CA TYR V 462 " pdb=" N TYR V 462 " pdb=" C TYR V 462 " pdb=" CB TYR V 462 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 chirality pdb=" CA VAL T 359 " pdb=" N VAL T 359 " pdb=" C VAL T 359 " pdb=" CB VAL T 359 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 7285 not shown) Planarity restraints: 6836 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE T 304 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO T 305 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO T 305 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO T 305 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU M 998 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C LEU M 998 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU M 998 " 0.013 2.00e-02 2.50e+03 pdb=" N PHE M 999 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP V 182 " 0.031 5.00e-02 4.00e+02 4.75e-02 3.61e+00 pdb=" N PRO V 183 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO V 183 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO V 183 " 0.027 5.00e-02 4.00e+02 ... (remaining 6833 not shown) Histogram of nonbonded interaction distances: 1.49 - 2.17: 10 2.17 - 2.85: 14055 2.85 - 3.54: 60353 3.54 - 4.22: 103596 4.22 - 4.90: 168414 Nonbonded interactions: 346428 Sorted by model distance: nonbonded pdb=" CE MET T 406 " pdb=" CD1 LEU T 418 " model vdw 1.491 3.880 nonbonded pdb=" OG1 THR Y 82 " pdb="MG MG Y 502 " model vdw 2.076 2.170 nonbonded pdb=" O1B ADP R 501 " pdb="MG MG R 503 " model vdw 2.077 2.170 nonbonded pdb=" N2 DG I -68 " pdb=" O2 DC J 68 " model vdw 2.132 2.496 nonbonded pdb=" OG1 THR U 162 " pdb=" O MET U 165 " model vdw 2.140 2.440 ... (remaining 346423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = (chain 'C' and resid 23 through 102) selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 17 through 117) selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 35 through 125) selection = chain 'H' } ncs_group { reference = (chain 'T' and (resid 22 through 150 or (resid 151 and (name N or name CA or nam \ e C or name O or name CB )) or resid 161 through 463 or resid 501)) selection = (chain 'V' and (resid 22 through 161 or (resid 162 through 163 and (name N or na \ me CA or name C or name O or name CB )) or resid 164 through 463 or resid 501)) selection = (chain 'X' and (resid 22 through 150 or (resid 151 and (name N or name CA or nam \ e C or name O or name CB )) or (resid 161 through 163 and (name N or name CA or \ name C or name O or name CB )) or resid 164 through 463 or resid 501)) } ncs_group { reference = (chain 'U' and (resid 15 through 136 or (resid 137 and (name N or name CA or nam \ e C or name O or name CB )) or resid 138 through 145 or (resid 146 through 150 a \ nd (name N or name CA or name C or name O or name CB )) or resid 151 through 152 \ or (resid 153 through 154 and (name N or name CA or name C or name O or name CB \ )) or resid 155 through 180 or (resid 181 and (name N or name CA or name C or n \ ame O or name CB )) or resid 182 through 222 or (resid 223 and (name N or name C \ A or name C or name O or name CB )) or resid 224 through 459)) selection = (chain 'W' and (resid 15 through 136 or (resid 137 and (name N or name CA or nam \ e C or name O or name CB )) or resid 138 through 145 or (resid 146 through 150 a \ nd (name N or name CA or name C or name O or name CB )) or resid 151 through 152 \ or (resid 153 through 154 and (name N or name CA or name C or name O or name CB \ )) or resid 155 through 180 or (resid 181 and (name N or name CA or name C or n \ ame O or name CB )) or resid 182 through 200 or (resid 201 and (name N or name C \ A or name C or name O or name CB )) or resid 202 through 205 or resid 222 throug \ h 459)) selection = (chain 'Y' and (resid 15 through 200 or (resid 201 and (name N or name CA or nam \ e C or name O or name CB )) or resid 202 through 205 or resid 222 or (resid 223 \ and (name N or name CA or name C or name O or name CB )) or resid 224 through 45 \ 9)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.060 Extract box with map and model: 14.650 Check model and map are aligned: 0.550 Set scattering table: 0.350 Process input model: 148.540 Find NCS groups from input model: 2.460 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 178.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 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 0.086 44998 Z= 0.153 Angle : 0.621 12.807 62207 Z= 0.365 Chirality : 0.037 0.173 7288 Planarity : 0.003 0.056 6836 Dihedral : 18.743 179.465 17579 Min Nonbonded Distance : 1.491 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.60 % Favored : 95.36 % Rotamer: Outliers : 3.93 % Allowed : 7.97 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.02 % 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: -2.70 (0.10), residues: 4633 helix: -2.29 (0.08), residues: 2159 sheet: -0.39 (0.18), residues: 655 loop : -1.42 (0.12), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 790 HIS 0.009 0.001 HIS W 153 PHE 0.011 0.001 PHE Y 221 TYR 0.016 0.001 TYR V 462 ARG 0.005 0.000 ARG M1133 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 966 time to evaluate : 4.129 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: A 46 VAL cc_start: 0.8302 (t) cc_final: 0.7982 (t) REVERT: A 56 LYS cc_start: 0.7125 (mttm) cc_final: 0.6476 (tttm) REVERT: A 78 PHE cc_start: 0.4966 (m-10) cc_final: 0.4196 (m-80) REVERT: A 83 ARG cc_start: 0.7876 (mmt180) cc_final: 0.7498 (ttt180) REVERT: B 68 GLN cc_start: 0.7907 (tp40) cc_final: 0.7574 (tt0) REVERT: C 58 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8331 (tp) REVERT: C 59 LYS cc_start: 0.8371 (ttpt) cc_final: 0.7974 (tttp) REVERT: C 71 THR cc_start: 0.8378 (m) cc_final: 0.8004 (p) REVERT: C 91 LYS cc_start: 0.9007 (tppt) cc_final: 0.8524 (pptt) REVERT: D 35 ARG cc_start: 0.6704 (ttm-80) cc_final: 0.6495 (ttm110) REVERT: D 53 GLU cc_start: 0.7633 (tp30) cc_final: 0.6729 (mm-30) REVERT: D 64 SER cc_start: 0.9006 (m) cc_final: 0.8752 (t) REVERT: D 92 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.6616 (mtp-110) REVERT: E 43 ARG cc_start: 0.5814 (tpp80) cc_final: 0.5521 (ttp-170) REVERT: E 58 TYR cc_start: 0.7268 (t80) cc_final: 0.7029 (t80) REVERT: E 82 ARG cc_start: 0.7948 (ttt-90) cc_final: 0.7651 (ttt90) REVERT: F 26 PHE cc_start: 0.7298 (m-80) cc_final: 0.6729 (m-80) REVERT: F 30 ARG cc_start: 0.4050 (mmt90) cc_final: 0.3668 (mpt180) REVERT: F 36 ARG cc_start: 0.6370 (ttm110) cc_final: 0.5966 (mmm-85) REVERT: F 102 THR cc_start: 0.9021 (m) cc_final: 0.8714 (p) REVERT: G 74 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7696 (tm-30) REVERT: G 89 LYS cc_start: 0.5891 (mttt) cc_final: 0.5342 (ptmt) REVERT: G 109 LEU cc_start: 0.8783 (mt) cc_final: 0.8326 (mm) REVERT: H 46 LYS cc_start: 0.7145 (mttt) cc_final: 0.6858 (ttmm) REVERT: H 70 ASN cc_start: 0.7406 (t0) cc_final: 0.6816 (t0) REVERT: M 848 ARG cc_start: 0.6693 (mtt90) cc_final: 0.6119 (mtt90) REVERT: M 980 MET cc_start: 0.7365 (mmt) cc_final: 0.6267 (ptp) REVERT: M 1082 ASN cc_start: 0.5809 (OUTLIER) cc_final: 0.5593 (m-40) REVERT: M 1199 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9055 (pp) REVERT: R 3 THR cc_start: 0.7916 (OUTLIER) cc_final: 0.7693 (p) REVERT: R 66 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6782 (pt) REVERT: R 70 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6675 (pm20) REVERT: R 190 VAL cc_start: 0.8775 (t) cc_final: 0.8483 (m) REVERT: R 199 TRP cc_start: 0.7195 (m100) cc_final: 0.6739 (m100) REVERT: R 331 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7950 (t) REVERT: R 345 VAL cc_start: 0.7853 (OUTLIER) cc_final: 0.7644 (m) REVERT: S 202 LEU cc_start: 0.3756 (mt) cc_final: 0.3452 (mm) REVERT: S 220 MET cc_start: 0.7013 (ttp) cc_final: 0.5952 (tpt) REVERT: T 375 TYR cc_start: 0.6578 (m-80) cc_final: 0.6079 (m-80) REVERT: U 81 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.6948 (ttpt) REVERT: U 158 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9064 (pt) REVERT: V 342 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.7758 (mtt90) REVERT: V 344 MET cc_start: 0.9293 (mmm) cc_final: 0.9091 (mmm) REVERT: V 365 ASP cc_start: 0.7974 (OUTLIER) cc_final: 0.7630 (m-30) REVERT: W 149 ILE cc_start: 0.7536 (OUTLIER) cc_final: 0.7000 (tp) REVERT: W 164 ASP cc_start: 0.7080 (m-30) cc_final: 0.6379 (p0) REVERT: W 175 MET cc_start: 0.8714 (mmm) cc_final: 0.8497 (tpp) REVERT: W 323 MET cc_start: 0.7918 (mtt) cc_final: 0.7711 (mtt) REVERT: X 85 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8301 (mtmm) REVERT: X 210 LYS cc_start: 0.8120 (tttt) cc_final: 0.7875 (tppt) REVERT: X 312 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: Y 23 HIS cc_start: 0.8288 (OUTLIER) cc_final: 0.7870 (p90) REVERT: Y 310 ASN cc_start: 0.7707 (m-40) cc_final: 0.7401 (m110) outliers start: 157 outliers final: 35 residues processed: 1091 average time/residue: 0.6202 time to fit residues: 1054.3874 Evaluate side-chains 463 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 411 time to evaluate : 4.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 867 LEU Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1062 ILE Chi-restraints excluded: chain M residue 1082 ASN Chi-restraints excluded: chain M residue 1199 LEU Chi-restraints excluded: chain R residue 3 THR Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 66 LEU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 331 VAL Chi-restraints excluded: chain R residue 345 VAL Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 182 THR Chi-restraints excluded: chain T residue 256 ASN Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 81 LYS Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 400 SER Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 244 VAL Chi-restraints excluded: chain V residue 342 ARG Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 365 ASP Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 85 LYS Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 195 SER Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 417 GLN Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 220 ARG Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Y residue 352 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 426 optimal weight: 3.9990 chunk 382 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 chunk 130 optimal weight: 0.2980 chunk 258 optimal weight: 8.9990 chunk 204 optimal weight: 0.9980 chunk 395 optimal weight: 3.9990 chunk 153 optimal weight: 20.0000 chunk 240 optimal weight: 1.9990 chunk 294 optimal weight: 3.9990 chunk 458 optimal weight: 0.1980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 HIS E 42 GLN E 74 ASN F 39 ASN ** G 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 52 HIS H 112 HIS M 716 ASN ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 857 GLN M 940 GLN M1058 HIS M1226 GLN M1283 ASN M1302 GLN ** M1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 45 HIS R 98 HIS R 251 GLN R 374 GLN S 176 GLN T 256 ASN T 271 GLN U 119 GLN U 252 GLN U 451 GLN V 27 HIS V 124 ASN ** V 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 63 ASN W 455 GLN ** X 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 238 HIS X 256 ASN ** X 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 23 HIS Y 36 GLN Y 144 GLN Y 223 GLN Y 272 GLN ** Y 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 407 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 451 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 44998 Z= 0.260 Angle : 0.663 11.310 62207 Z= 0.342 Chirality : 0.042 0.242 7288 Planarity : 0.005 0.058 6836 Dihedral : 23.044 151.544 8728 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.87 % Favored : 97.11 % Rotamer: Outliers : 4.71 % Allowed : 14.08 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.24 (0.11), residues: 4633 helix: -0.58 (0.10), residues: 2170 sheet: -0.03 (0.18), residues: 691 loop : -1.29 (0.13), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP R 199 HIS 0.009 0.001 HIS E 32 PHE 0.022 0.002 PHE G 68 TYR 0.021 0.002 TYR D 88 ARG 0.010 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 426 time to evaluate : 4.660 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: B 53 ARG cc_start: 0.7284 (ttm170) cc_final: 0.6860 (mtt90) REVERT: C 62 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.8060 (mm) REVERT: C 71 THR cc_start: 0.8576 (m) cc_final: 0.8145 (p) REVERT: C 77 LYS cc_start: 0.8297 (mmmm) cc_final: 0.7517 (mptt) REVERT: D 53 GLU cc_start: 0.7361 (tp30) cc_final: 0.6772 (mm-30) REVERT: D 63 GLU cc_start: 0.7838 (tm-30) cc_final: 0.7547 (tm-30) REVERT: D 92 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.6503 (mtp-110) REVERT: E 43 ARG cc_start: 0.6120 (tpp80) cc_final: 0.5794 (ttp-170) REVERT: E 72 ARG cc_start: 0.8156 (mmm160) cc_final: 0.7794 (mmm160) REVERT: F 26 PHE cc_start: 0.7050 (m-80) cc_final: 0.6595 (m-80) REVERT: F 36 ARG cc_start: 0.6139 (ttm110) cc_final: 0.5822 (mmm-85) REVERT: F 102 THR cc_start: 0.8982 (m) cc_final: 0.8735 (p) REVERT: G 74 GLU cc_start: 0.8222 (mm-30) cc_final: 0.7774 (tm-30) REVERT: G 89 LYS cc_start: 0.5771 (mttt) cc_final: 0.5162 (ptmm) REVERT: G 103 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.7061 (pp) REVERT: G 109 LEU cc_start: 0.8876 (mt) cc_final: 0.8542 (mm) REVERT: H 49 LYS cc_start: 0.6546 (mmmt) cc_final: 0.6161 (mttp) REVERT: H 62 MET cc_start: 0.6355 (tmm) cc_final: 0.6146 (ttt) REVERT: M 848 ARG cc_start: 0.6373 (mtt90) cc_final: 0.5880 (mtt90) REVERT: M 980 MET cc_start: 0.7760 (mmt) cc_final: 0.6663 (ptt) REVERT: M 987 MET cc_start: 0.7598 (tpp) cc_final: 0.7349 (tpp) REVERT: M 1082 ASN cc_start: 0.5874 (OUTLIER) cc_final: 0.5649 (m-40) REVERT: M 1111 LYS cc_start: 0.7581 (ttmt) cc_final: 0.7339 (tptm) REVERT: R 229 GLU cc_start: 0.7125 (tp30) cc_final: 0.6873 (tp30) REVERT: S 170 GLU cc_start: 0.7815 (tp30) cc_final: 0.7604 (tp30) REVERT: S 179 TYR cc_start: 0.6636 (OUTLIER) cc_final: 0.6390 (p90) REVERT: S 220 MET cc_start: 0.6859 (ttp) cc_final: 0.5889 (tpt) REVERT: T 151 ASP cc_start: 0.8081 (p0) cc_final: 0.7870 (p0) REVERT: U 31 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6947 (mp) REVERT: U 158 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8830 (pt) REVERT: U 301 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8422 (mp) REVERT: V 177 LYS cc_start: 0.7927 (mtpp) cc_final: 0.7642 (mtpp) REVERT: V 220 THR cc_start: 0.7182 (m) cc_final: 0.6953 (p) REVERT: V 365 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7753 (m-30) REVERT: W 164 ASP cc_start: 0.7419 (m-30) cc_final: 0.6440 (p0) REVERT: W 175 MET cc_start: 0.8704 (mmm) cc_final: 0.8253 (tpp) REVERT: X 135 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6945 (mm-30) REVERT: X 210 LYS cc_start: 0.8392 (tttt) cc_final: 0.8172 (tppt) REVERT: X 312 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: Y 310 ASN cc_start: 0.7762 (m-40) cc_final: 0.7513 (m110) REVERT: Y 341 HIS cc_start: 0.7616 (OUTLIER) cc_final: 0.6826 (t70) outliers start: 188 outliers final: 101 residues processed: 588 average time/residue: 0.5584 time to fit residues: 530.8643 Evaluate side-chains 435 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 323 time to evaluate : 4.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 36 ARG Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 738 LEU Chi-restraints excluded: chain M residue 752 VAL Chi-restraints excluded: chain M residue 758 LEU Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 867 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1001 VAL Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1062 ILE Chi-restraints excluded: chain M residue 1082 ASN Chi-restraints excluded: chain M residue 1340 ASP Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 120 PHE Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 239 MET Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 316 THR Chi-restraints excluded: chain R residue 417 GLU Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 179 TYR Chi-restraints excluded: chain S residue 182 THR Chi-restraints excluded: chain S residue 263 ILE Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 154 ASN Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 31 LEU Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 300 MET Chi-restraints excluded: chain U residue 301 LEU Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 386 LEU Chi-restraints excluded: chain U residue 400 SER Chi-restraints excluded: chain V residue 56 GLU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 237 VAL Chi-restraints excluded: chain V residue 244 VAL Chi-restraints excluded: chain V residue 303 LEU Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 365 ASP Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 401 ASP Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 435 VAL Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 27 THR Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 196 SER Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 195 SER Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 297 ASP Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 378 ASP Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 417 GLN Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 220 ARG Chi-restraints excluded: chain Y residue 257 LEU Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 437 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 254 optimal weight: 0.8980 chunk 142 optimal weight: 3.9990 chunk 381 optimal weight: 4.9990 chunk 312 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 459 optimal weight: 0.9990 chunk 496 optimal weight: 2.9990 chunk 409 optimal weight: 1.9990 chunk 455 optimal weight: 0.6980 chunk 156 optimal weight: 0.5980 chunk 368 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 ASN G 98 GLN M 712 ASN M 730 GLN ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 124 ASN ** V 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 417 GLN W 299 HIS ** X 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 44998 Z= 0.182 Angle : 0.587 10.277 62207 Z= 0.302 Chirality : 0.039 0.213 7288 Planarity : 0.004 0.062 6836 Dihedral : 22.846 152.075 8697 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.43 % Favored : 96.55 % Rotamer: Outliers : 4.43 % Allowed : 15.13 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.58 (0.12), residues: 4633 helix: 0.17 (0.11), residues: 2152 sheet: 0.07 (0.18), residues: 690 loop : -1.14 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 818 HIS 0.010 0.001 HIS R 430 PHE 0.021 0.001 PHE G 68 TYR 0.031 0.001 TYR M 699 ARG 0.008 0.000 ARG H 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 374 time to evaluate : 4.403 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: symmetry clash REVERT: A 83 ARG cc_start: 0.8011 (mmt180) cc_final: 0.7496 (ttt180) REVERT: B 53 ARG cc_start: 0.7215 (ttm170) cc_final: 0.6712 (mtt90) REVERT: C 44 LYS cc_start: 0.7074 (tptp) cc_final: 0.6727 (tppt) REVERT: C 71 THR cc_start: 0.8588 (m) cc_final: 0.8202 (p) REVERT: C 77 LYS cc_start: 0.8229 (mmmm) cc_final: 0.7495 (mptt) REVERT: D 53 GLU cc_start: 0.7259 (tp30) cc_final: 0.6756 (mm-30) REVERT: D 63 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7422 (tm-30) REVERT: D 92 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.6618 (mtp-110) REVERT: E 43 ARG cc_start: 0.6139 (tpp80) cc_final: 0.5883 (ttp-170) REVERT: E 72 ARG cc_start: 0.8200 (mmm160) cc_final: 0.7840 (mmm160) REVERT: F 26 PHE cc_start: 0.7190 (m-80) cc_final: 0.6660 (m-80) REVERT: F 36 ARG cc_start: 0.6294 (ttm110) cc_final: 0.6056 (mmm-85) REVERT: F 37 ARG cc_start: 0.8225 (mmm160) cc_final: 0.6747 (mtt180) REVERT: F 95 ASN cc_start: 0.7645 (t0) cc_final: 0.7352 (t0) REVERT: F 102 THR cc_start: 0.8975 (m) cc_final: 0.8668 (p) REVERT: G 74 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7752 (tm-30) REVERT: G 89 LYS cc_start: 0.5659 (mttt) cc_final: 0.5093 (ptmm) REVERT: G 103 LEU cc_start: 0.7483 (OUTLIER) cc_final: 0.7198 (pp) REVERT: G 109 LEU cc_start: 0.8873 (mt) cc_final: 0.8602 (mm) REVERT: H 49 LYS cc_start: 0.6548 (mmmt) cc_final: 0.6138 (mttp) REVERT: H 71 ASP cc_start: 0.7800 (t0) cc_final: 0.7214 (t0) REVERT: H 86 TYR cc_start: 0.6757 (m-10) cc_final: 0.6448 (m-80) REVERT: M 762 MET cc_start: 0.7601 (ppp) cc_final: 0.7393 (ppp) REVERT: M 870 LEU cc_start: 0.7539 (mt) cc_final: 0.7262 (mt) REVERT: M 980 MET cc_start: 0.7896 (mmt) cc_final: 0.6728 (ptp) REVERT: M 1082 ASN cc_start: 0.6136 (OUTLIER) cc_final: 0.5703 (m-40) REVERT: M 1135 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7937 (tt) REVERT: S 220 MET cc_start: 0.6895 (ttp) cc_final: 0.5886 (tpt) REVERT: U 301 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8383 (mp) REVERT: V 318 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8521 (tt) REVERT: V 362 ASP cc_start: 0.7774 (OUTLIER) cc_final: 0.7420 (p0) REVERT: V 365 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7578 (m-30) REVERT: W 86 MET cc_start: 0.8169 (tpt) cc_final: 0.7853 (tpp) REVERT: W 175 MET cc_start: 0.8693 (mmm) cc_final: 0.8258 (tpp) REVERT: X 210 LYS cc_start: 0.8433 (tttt) cc_final: 0.8184 (tppt) REVERT: X 246 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7275 (p0) REVERT: X 312 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: X 344 MET cc_start: 0.8141 (mmt) cc_final: 0.7870 (mmp) REVERT: X 406 MET cc_start: 0.8015 (ttp) cc_final: 0.7609 (mtm) REVERT: Y 310 ASN cc_start: 0.7706 (m-40) cc_final: 0.7409 (m110) outliers start: 177 outliers final: 102 residues processed: 523 average time/residue: 0.5768 time to fit residues: 493.5421 Evaluate side-chains 429 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 317 time to evaluate : 4.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 95 ARG Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 738 LEU Chi-restraints excluded: chain M residue 752 VAL Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 867 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1007 SER Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1082 ASN Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1135 ILE Chi-restraints excluded: chain M residue 1205 VAL Chi-restraints excluded: chain M residue 1245 CYS Chi-restraints excluded: chain M residue 1276 ASP Chi-restraints excluded: chain M residue 1340 ASP Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 182 THR Chi-restraints excluded: chain S residue 263 ILE Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 154 ASN Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 353 VAL Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 301 LEU Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 386 LEU Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 237 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 302 GLU Chi-restraints excluded: chain V residue 318 ILE Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 362 ASP Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 365 ASP Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 417 GLN Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 386 LEU Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 195 SER Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 246 ASP Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 297 ASP Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 417 GLN Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 220 ARG Chi-restraints excluded: chain Y residue 257 LEU Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 437 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 453 optimal weight: 4.9990 chunk 345 optimal weight: 0.2980 chunk 238 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 219 optimal weight: 0.8980 chunk 308 optimal weight: 3.9990 chunk 461 optimal weight: 5.9990 chunk 488 optimal weight: 0.9990 chunk 240 optimal weight: 3.9990 chunk 436 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 27 GLN G 98 GLN ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1082 ASN M1350 GLN ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 HIS S 97 GLN U 155 GLN V 27 HIS V 124 ASN ** V 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 263 GLN V 271 GLN W 230 GLN ** X 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 271 GLN Y 242 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 44998 Z= 0.235 Angle : 0.607 9.984 62207 Z= 0.312 Chirality : 0.040 0.198 7288 Planarity : 0.004 0.053 6836 Dihedral : 22.773 152.968 8693 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.58 % Favored : 96.40 % Rotamer: Outliers : 4.68 % Allowed : 15.56 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.34 (0.12), residues: 4633 helix: 0.46 (0.11), residues: 2150 sheet: 0.02 (0.19), residues: 683 loop : -1.07 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 818 HIS 0.005 0.001 HIS E 32 PHE 0.021 0.002 PHE M1317 TYR 0.031 0.002 TYR M 699 ARG 0.011 0.001 ARG T 431 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 345 time to evaluate : 5.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8043 (mmt180) cc_final: 0.7423 (ttt180) REVERT: B 53 ARG cc_start: 0.7113 (ttm170) cc_final: 0.6770 (mtt90) REVERT: B 59 GLU cc_start: 0.7973 (pp20) cc_final: 0.7624 (pp20) REVERT: C 44 LYS cc_start: 0.7042 (tptp) cc_final: 0.6611 (tppt) REVERT: C 71 THR cc_start: 0.8690 (m) cc_final: 0.8357 (p) REVERT: C 77 LYS cc_start: 0.8168 (mmmm) cc_final: 0.7370 (mptt) REVERT: D 53 GLU cc_start: 0.7361 (tp30) cc_final: 0.6804 (mm-30) REVERT: D 63 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7355 (tm-30) REVERT: D 92 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7079 (ptm160) REVERT: E 43 ARG cc_start: 0.6156 (tpp80) cc_final: 0.5894 (ttp-170) REVERT: F 26 PHE cc_start: 0.7252 (m-80) cc_final: 0.6590 (m-80) REVERT: F 36 ARG cc_start: 0.6175 (ttm110) cc_final: 0.5945 (mmm-85) REVERT: F 37 ARG cc_start: 0.8265 (mmm160) cc_final: 0.6783 (mtt180) REVERT: F 96 LYS cc_start: 0.6818 (tppt) cc_final: 0.6414 (mtmt) REVERT: F 102 THR cc_start: 0.8977 (m) cc_final: 0.8617 (p) REVERT: G 48 LEU cc_start: 0.8979 (tp) cc_final: 0.8689 (tp) REVERT: G 74 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7775 (tm-30) REVERT: G 89 LYS cc_start: 0.5554 (mttt) cc_final: 0.5025 (ptmm) REVERT: G 103 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7235 (pp) REVERT: H 49 LYS cc_start: 0.6494 (mmmt) cc_final: 0.5988 (mttp) REVERT: M 762 MET cc_start: 0.7595 (ppp) cc_final: 0.7373 (ppp) REVERT: M 870 LEU cc_start: 0.7391 (mt) cc_final: 0.7158 (mt) REVERT: M 980 MET cc_start: 0.7956 (mmt) cc_final: 0.6836 (ptp) REVERT: M 1280 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7879 (tm-30) REVERT: S 170 GLU cc_start: 0.7800 (tp30) cc_final: 0.7513 (tp30) REVERT: S 220 MET cc_start: 0.6981 (ttp) cc_final: 0.5981 (tpt) REVERT: U 301 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8475 (mp) REVERT: U 349 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7797 (t0) REVERT: W 86 MET cc_start: 0.8255 (tpt) cc_final: 0.7829 (tpp) REVERT: W 175 MET cc_start: 0.8719 (mmm) cc_final: 0.8303 (tpp) REVERT: X 210 LYS cc_start: 0.8441 (tttt) cc_final: 0.8188 (tppt) REVERT: X 246 ASP cc_start: 0.7742 (OUTLIER) cc_final: 0.7286 (p0) REVERT: X 312 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: X 344 MET cc_start: 0.8269 (mmt) cc_final: 0.7948 (mmp) REVERT: Y 310 ASN cc_start: 0.7867 (m-40) cc_final: 0.7526 (m110) outliers start: 187 outliers final: 130 residues processed: 504 average time/residue: 0.5678 time to fit residues: 468.4562 Evaluate side-chains 438 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 302 time to evaluate : 3.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 29 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 93 SER Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 738 LEU Chi-restraints excluded: chain M residue 752 VAL Chi-restraints excluded: chain M residue 832 PHE Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 867 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1006 THR Chi-restraints excluded: chain M residue 1007 SER Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1062 ILE Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1197 LEU Chi-restraints excluded: chain M residue 1205 VAL Chi-restraints excluded: chain M residue 1276 ASP Chi-restraints excluded: chain M residue 1340 ASP Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 400 MET Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 103 MET Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 126 VAL Chi-restraints excluded: chain S residue 179 TYR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 263 ILE Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 154 ASN Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 301 LEU Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 349 ASP Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 386 LEU Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 220 THR Chi-restraints excluded: chain V residue 237 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 286 GLN Chi-restraints excluded: chain V residue 302 GLU Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 417 GLN Chi-restraints excluded: chain V residue 436 VAL Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 196 SER Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 350 ARG Chi-restraints excluded: chain W residue 353 ILE Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 246 ASP Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 297 ASP Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 417 GLN Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 220 ARG Chi-restraints excluded: chain Y residue 257 LEU Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 413 ARG Chi-restraints excluded: chain Y residue 437 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 406 optimal weight: 2.9990 chunk 277 optimal weight: 0.2980 chunk 7 optimal weight: 9.9990 chunk 363 optimal weight: 0.9980 chunk 201 optimal weight: 0.9980 chunk 416 optimal weight: 0.0060 chunk 337 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 chunk 249 optimal weight: 6.9990 chunk 438 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 712 ASN ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1356 HIS U 153 HIS V 124 ASN V 205 ASN ** V 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 417 GLN W 23 HIS ** Y 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 44998 Z= 0.154 Angle : 0.571 10.142 62207 Z= 0.292 Chirality : 0.039 0.191 7288 Planarity : 0.003 0.051 6836 Dihedral : 22.666 153.161 8686 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.37 % Favored : 96.59 % Rotamer: Outliers : 3.91 % Allowed : 16.96 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.06 (0.12), residues: 4633 helix: 0.73 (0.11), residues: 2158 sheet: 0.12 (0.19), residues: 678 loop : -0.97 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 760 HIS 0.006 0.001 HIS U 153 PHE 0.036 0.001 PHE G 68 TYR 0.033 0.001 TYR M 699 ARG 0.006 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 337 time to evaluate : 4.933 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: A 83 ARG cc_start: 0.8045 (mmt180) cc_final: 0.7455 (mmm-85) REVERT: B 53 ARG cc_start: 0.7089 (ttm170) cc_final: 0.6833 (mtt90) REVERT: B 59 GLU cc_start: 0.7993 (pp20) cc_final: 0.7674 (pp20) REVERT: C 71 THR cc_start: 0.8707 (m) cc_final: 0.8409 (p) REVERT: C 77 LYS cc_start: 0.8131 (mmmm) cc_final: 0.7438 (mptt) REVERT: D 53 GLU cc_start: 0.7361 (tp30) cc_final: 0.6799 (mm-30) REVERT: D 63 GLU cc_start: 0.7587 (tm-30) cc_final: 0.7312 (tm-30) REVERT: D 92 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7068 (ptm160) REVERT: E 30 ARG cc_start: 0.8268 (mtt180) cc_final: 0.8029 (mtm180) REVERT: E 43 ARG cc_start: 0.6180 (tpp80) cc_final: 0.5948 (ttp-170) REVERT: E 72 ARG cc_start: 0.8270 (mmm160) cc_final: 0.7817 (mmm160) REVERT: F 26 PHE cc_start: 0.7239 (m-80) cc_final: 0.6530 (m-80) REVERT: F 36 ARG cc_start: 0.6155 (ttm110) cc_final: 0.5827 (mmm-85) REVERT: F 37 ARG cc_start: 0.8264 (mmm160) cc_final: 0.6927 (ttm110) REVERT: F 102 THR cc_start: 0.8965 (m) cc_final: 0.8606 (p) REVERT: G 48 LEU cc_start: 0.8944 (tp) cc_final: 0.8733 (tp) REVERT: G 89 LYS cc_start: 0.5620 (mttt) cc_final: 0.5067 (ptmm) REVERT: G 103 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7337 (pp) REVERT: H 49 LYS cc_start: 0.6513 (mmmt) cc_final: 0.6142 (mttp) REVERT: H 95 ARG cc_start: 0.7937 (mmm160) cc_final: 0.7613 (mmm160) REVERT: M 762 MET cc_start: 0.7575 (ppp) cc_final: 0.7340 (ppp) REVERT: M 980 MET cc_start: 0.7947 (mmt) cc_final: 0.7625 (mmt) REVERT: M 1135 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7945 (tt) REVERT: M 1280 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7869 (tm-30) REVERT: M 1339 TYR cc_start: 0.6996 (OUTLIER) cc_final: 0.6243 (m-80) REVERT: S 170 GLU cc_start: 0.7653 (tp30) cc_final: 0.7323 (tp30) REVERT: S 220 MET cc_start: 0.6953 (ttp) cc_final: 0.5972 (tpt) REVERT: U 283 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7033 (mp0) REVERT: U 301 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8382 (mp) REVERT: V 77 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.8300 (mt) REVERT: V 272 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.9086 (tt) REVERT: W 86 MET cc_start: 0.8228 (tpt) cc_final: 0.7927 (tpp) REVERT: W 175 MET cc_start: 0.8683 (mmm) cc_final: 0.8301 (tpp) REVERT: X 210 LYS cc_start: 0.8458 (tttt) cc_final: 0.8200 (tppt) REVERT: X 246 ASP cc_start: 0.7797 (OUTLIER) cc_final: 0.7345 (p0) REVERT: X 312 GLU cc_start: 0.8463 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: X 344 MET cc_start: 0.8322 (mmt) cc_final: 0.7970 (mmp) REVERT: Y 58 LEU cc_start: 0.9074 (tp) cc_final: 0.8812 (tt) REVERT: Y 310 ASN cc_start: 0.7794 (m-40) cc_final: 0.7416 (m110) REVERT: Y 411 MET cc_start: 0.7828 (OUTLIER) cc_final: 0.7579 (mtp) outliers start: 156 outliers final: 111 residues processed: 467 average time/residue: 0.5515 time to fit residues: 422.7742 Evaluate side-chains 426 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 304 time to evaluate : 4.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 80 ILE Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 738 LEU Chi-restraints excluded: chain M residue 752 VAL Chi-restraints excluded: chain M residue 805 LEU Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 867 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1007 SER Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1062 ILE Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1135 ILE Chi-restraints excluded: chain M residue 1245 CYS Chi-restraints excluded: chain M residue 1276 ASP Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 239 MET Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 417 GLU Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 103 MET Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 179 TYR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 263 ILE Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 154 ASN Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 135 LEU Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 202 LEU Chi-restraints excluded: chain U residue 283 GLU Chi-restraints excluded: chain U residue 301 LEU Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 386 LEU Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 77 LEU Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 302 GLU Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 417 GLN Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 86 THR Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 246 ASP Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 332 ILE Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 417 GLN Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 220 ARG Chi-restraints excluded: chain Y residue 257 LEU Chi-restraints excluded: chain Y residue 341 HIS Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Y residue 413 ARG Chi-restraints excluded: chain Y residue 437 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 164 optimal weight: 5.9990 chunk 439 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 286 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 488 optimal weight: 6.9990 chunk 405 optimal weight: 0.0470 chunk 226 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 161 optimal weight: 2.9990 chunk 256 optimal weight: 7.9990 overall best weight: 1.8084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 42 GLN ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 367 GLN U 25 HIS V 124 ASN ** V 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 357 HIS V 417 GLN W 63 ASN ** X 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 44998 Z= 0.270 Angle : 0.632 10.811 62207 Z= 0.325 Chirality : 0.041 0.236 7288 Planarity : 0.004 0.053 6836 Dihedral : 22.679 154.306 8682 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.19 % Favored : 95.77 % Rotamer: Outliers : 4.46 % Allowed : 16.91 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.19 (0.12), residues: 4633 helix: 0.69 (0.11), residues: 2142 sheet: -0.12 (0.19), residues: 669 loop : -1.02 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 760 HIS 0.006 0.001 HIS M1225 PHE 0.036 0.002 PHE G 68 TYR 0.031 0.002 TYR M 699 ARG 0.005 0.001 ARG F 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 315 time to evaluate : 4.492 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8105 (mmt180) cc_final: 0.7520 (mmm-85) REVERT: B 53 ARG cc_start: 0.7093 (ttm170) cc_final: 0.6845 (mtt90) REVERT: B 59 GLU cc_start: 0.8051 (pp20) cc_final: 0.7708 (pp20) REVERT: C 71 THR cc_start: 0.8717 (m) cc_final: 0.8460 (p) REVERT: C 77 LYS cc_start: 0.8115 (mmmm) cc_final: 0.7400 (mptt) REVERT: D 53 GLU cc_start: 0.7495 (tp30) cc_final: 0.6911 (mm-30) REVERT: D 63 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7247 (tm-30) REVERT: D 92 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7153 (ptm160) REVERT: E 43 ARG cc_start: 0.6205 (tpp80) cc_final: 0.5950 (ttp-170) REVERT: E 72 ARG cc_start: 0.8278 (mmm160) cc_final: 0.7849 (mmm160) REVERT: F 26 PHE cc_start: 0.7329 (m-80) cc_final: 0.6442 (m-80) REVERT: F 37 ARG cc_start: 0.8343 (mmm160) cc_final: 0.6848 (mtt180) REVERT: F 96 LYS cc_start: 0.6766 (tppt) cc_final: 0.6235 (mtmt) REVERT: F 102 THR cc_start: 0.8827 (m) cc_final: 0.8423 (p) REVERT: G 48 LEU cc_start: 0.8904 (tp) cc_final: 0.8596 (tp) REVERT: G 89 LYS cc_start: 0.5715 (mttt) cc_final: 0.5186 (ptmm) REVERT: G 103 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7387 (pp) REVERT: H 49 LYS cc_start: 0.6521 (mmmt) cc_final: 0.6023 (mttp) REVERT: M 762 MET cc_start: 0.7636 (ppp) cc_final: 0.7396 (ppp) REVERT: M 980 MET cc_start: 0.7938 (mmt) cc_final: 0.7550 (mmt) REVERT: M 1280 GLN cc_start: 0.8174 (tm-30) cc_final: 0.7879 (tm-30) REVERT: M 1339 TYR cc_start: 0.7187 (OUTLIER) cc_final: 0.6305 (m-80) REVERT: S 103 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7051 (mtp) REVERT: S 170 GLU cc_start: 0.7651 (tp30) cc_final: 0.7332 (tp30) REVERT: S 220 MET cc_start: 0.6794 (ttp) cc_final: 0.5818 (tpt) REVERT: T 70 MET cc_start: 0.7866 (mmm) cc_final: 0.7509 (mmm) REVERT: U 164 ASP cc_start: 0.7307 (t70) cc_final: 0.6963 (t70) REVERT: U 349 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7764 (t0) REVERT: W 86 MET cc_start: 0.8280 (tpt) cc_final: 0.7850 (tpp) REVERT: W 175 MET cc_start: 0.8710 (mmm) cc_final: 0.8377 (tpp) REVERT: X 210 LYS cc_start: 0.8624 (tttt) cc_final: 0.8260 (tppt) REVERT: X 246 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7395 (p0) REVERT: X 312 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: Y 310 ASN cc_start: 0.7957 (m-40) cc_final: 0.7557 (m110) REVERT: Y 411 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.7549 (mtp) outliers start: 178 outliers final: 140 residues processed: 464 average time/residue: 0.5808 time to fit residues: 440.3031 Evaluate side-chains 441 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 293 time to evaluate : 4.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 738 LEU Chi-restraints excluded: chain M residue 752 VAL Chi-restraints excluded: chain M residue 805 LEU Chi-restraints excluded: chain M residue 832 PHE Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 867 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1007 SER Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1062 ILE Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1205 VAL Chi-restraints excluded: chain M residue 1276 ASP Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1340 ASP Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 239 MET Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 407 ASP Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 55 ASP Chi-restraints excluded: chain S residue 103 MET Chi-restraints excluded: chain S residue 113 LEU Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 179 TYR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 213 ASP Chi-restraints excluded: chain S residue 263 ILE Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 154 ASN Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 135 LEU Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 244 ILE Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 349 ASP Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 386 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 220 THR Chi-restraints excluded: chain V residue 228 GLU Chi-restraints excluded: chain V residue 252 LEU Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 303 LEU Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 410 THR Chi-restraints excluded: chain V residue 436 VAL Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 196 SER Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 350 ARG Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 353 ILE Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 136 THR Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 246 ASP Chi-restraints excluded: chain X residue 272 LEU Chi-restraints excluded: chain X residue 278 THR Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 332 ILE Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 378 ASP Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 417 GLN Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 171 LEU Chi-restraints excluded: chain Y residue 220 ARG Chi-restraints excluded: chain Y residue 222 VAL Chi-restraints excluded: chain Y residue 257 LEU Chi-restraints excluded: chain Y residue 313 LEU Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Y residue 437 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 471 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 278 optimal weight: 0.2980 chunk 356 optimal weight: 1.9990 chunk 276 optimal weight: 0.8980 chunk 411 optimal weight: 0.9990 chunk 272 optimal weight: 2.9990 chunk 486 optimal weight: 1.9990 chunk 304 optimal weight: 5.9990 chunk 296 optimal weight: 3.9990 chunk 224 optimal weight: 6.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 712 ASN M 811 HIS ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 124 ASN ** V 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 44998 Z= 0.206 Angle : 0.587 10.858 62207 Z= 0.302 Chirality : 0.040 0.179 7288 Planarity : 0.003 0.054 6836 Dihedral : 22.634 154.707 8675 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.93 % Favored : 96.01 % Rotamer: Outliers : 4.33 % Allowed : 17.33 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.09 (0.12), residues: 4633 helix: 0.81 (0.11), residues: 2149 sheet: -0.13 (0.19), residues: 676 loop : -1.01 (0.14), residues: 1808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 760 HIS 0.006 0.001 HIS T 250 PHE 0.029 0.001 PHE G 68 TYR 0.028 0.001 TYR D 88 ARG 0.011 0.000 ARG H 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 484 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 311 time to evaluate : 4.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8102 (mmt180) cc_final: 0.7536 (mmm-85) REVERT: B 53 ARG cc_start: 0.7085 (ttm170) cc_final: 0.6833 (mtt90) REVERT: B 59 GLU cc_start: 0.8044 (pp20) cc_final: 0.7711 (pp20) REVERT: C 71 THR cc_start: 0.8723 (m) cc_final: 0.8483 (p) REVERT: C 77 LYS cc_start: 0.8127 (mmmm) cc_final: 0.7405 (mptt) REVERT: D 53 GLU cc_start: 0.7514 (tp30) cc_final: 0.6927 (mm-30) REVERT: D 59 LYS cc_start: 0.8790 (mmmt) cc_final: 0.8371 (pttp) REVERT: D 63 GLU cc_start: 0.7537 (tm-30) cc_final: 0.7233 (tm-30) REVERT: D 92 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7117 (ptm160) REVERT: E 30 ARG cc_start: 0.8316 (mtt180) cc_final: 0.8048 (mtm180) REVERT: E 43 ARG cc_start: 0.6192 (tpp80) cc_final: 0.5953 (ttp-170) REVERT: E 72 ARG cc_start: 0.8262 (mmm160) cc_final: 0.7818 (mmm160) REVERT: F 26 PHE cc_start: 0.7374 (m-80) cc_final: 0.6502 (m-80) REVERT: F 96 LYS cc_start: 0.6689 (tppt) cc_final: 0.6163 (mtmt) REVERT: F 102 THR cc_start: 0.8821 (m) cc_final: 0.8416 (p) REVERT: G 89 LYS cc_start: 0.5631 (mttt) cc_final: 0.5171 (ptmm) REVERT: G 103 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7335 (pp) REVERT: H 39 THR cc_start: 0.5511 (t) cc_final: 0.4895 (p) REVERT: H 49 LYS cc_start: 0.6378 (mmmt) cc_final: 0.6079 (mttp) REVERT: H 95 ARG cc_start: 0.8000 (mmm160) cc_final: 0.7297 (mtt180) REVERT: M 762 MET cc_start: 0.7620 (ppp) cc_final: 0.7377 (ppp) REVERT: M 980 MET cc_start: 0.7977 (mmt) cc_final: 0.7551 (mmt) REVERT: M 1004 ILE cc_start: 0.7947 (mm) cc_final: 0.7652 (mm) REVERT: M 1280 GLN cc_start: 0.8219 (tm-30) cc_final: 0.7933 (tm-30) REVERT: M 1339 TYR cc_start: 0.7182 (OUTLIER) cc_final: 0.6322 (m-80) REVERT: R 147 MET cc_start: 0.6848 (mmm) cc_final: 0.6436 (tpt) REVERT: R 279 PHE cc_start: 0.6155 (OUTLIER) cc_final: 0.5904 (t80) REVERT: S 103 MET cc_start: 0.7331 (OUTLIER) cc_final: 0.7025 (mtp) REVERT: S 170 GLU cc_start: 0.7694 (tp30) cc_final: 0.7348 (tp30) REVERT: S 220 MET cc_start: 0.6849 (ttp) cc_final: 0.5892 (tpt) REVERT: T 70 MET cc_start: 0.7848 (mmm) cc_final: 0.7454 (mmm) REVERT: T 278 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8268 (p) REVERT: U 164 ASP cc_start: 0.7397 (OUTLIER) cc_final: 0.7035 (t70) REVERT: U 283 GLU cc_start: 0.7628 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: V 272 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8992 (tt) REVERT: W 175 MET cc_start: 0.8688 (mmm) cc_final: 0.8391 (tpp) REVERT: X 125 PHE cc_start: 0.8711 (OUTLIER) cc_final: 0.8322 (t80) REVERT: X 210 LYS cc_start: 0.8662 (tttt) cc_final: 0.8271 (tppt) REVERT: X 246 ASP cc_start: 0.7832 (OUTLIER) cc_final: 0.7382 (p0) REVERT: X 312 GLU cc_start: 0.8530 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: Y 310 ASN cc_start: 0.7886 (m-40) cc_final: 0.7476 (m110) REVERT: Y 411 MET cc_start: 0.7933 (OUTLIER) cc_final: 0.7602 (mtp) outliers start: 173 outliers final: 131 residues processed: 456 average time/residue: 0.5463 time to fit residues: 411.1721 Evaluate side-chains 434 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 290 time to evaluate : 4.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 738 LEU Chi-restraints excluded: chain M residue 752 VAL Chi-restraints excluded: chain M residue 803 TYR Chi-restraints excluded: chain M residue 805 LEU Chi-restraints excluded: chain M residue 811 HIS Chi-restraints excluded: chain M residue 821 MET Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 867 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1006 THR Chi-restraints excluded: chain M residue 1007 SER Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1062 ILE Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1276 ASP Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1340 ASP Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 239 MET Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 279 PHE Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 407 ASP Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 103 MET Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 179 TYR Chi-restraints excluded: chain S residue 182 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 263 ILE Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 75 ILE Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 135 GLU Chi-restraints excluded: chain T residue 154 ASN Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 135 LEU Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 164 ASP Chi-restraints excluded: chain U residue 283 GLU Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 386 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 220 THR Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 272 LEU Chi-restraints excluded: chain V residue 303 LEU Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 402 LEU Chi-restraints excluded: chain V residue 417 GLN Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 222 VAL Chi-restraints excluded: chain W residue 350 ARG Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 353 ILE Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 77 LEU Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 136 THR Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 237 VAL Chi-restraints excluded: chain X residue 246 ASP Chi-restraints excluded: chain X residue 300 VAL Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 332 ILE Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 378 ASP Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 417 GLN Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 171 LEU Chi-restraints excluded: chain Y residue 220 ARG Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 370 ILE Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Y residue 437 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 301 optimal weight: 8.9990 chunk 194 optimal weight: 0.9980 chunk 290 optimal weight: 0.0060 chunk 146 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 309 optimal weight: 0.9980 chunk 331 optimal weight: 5.9990 chunk 240 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 382 optimal weight: 4.9990 overall best weight: 1.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 42 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 712 ASN ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 417 GLN ** X 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.4363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 44998 Z= 0.245 Angle : 0.614 12.515 62207 Z= 0.315 Chirality : 0.040 0.179 7288 Planarity : 0.004 0.054 6836 Dihedral : 22.620 155.329 8673 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.38 % Favored : 95.55 % Rotamer: Outliers : 4.43 % Allowed : 17.54 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -0.14 (0.12), residues: 4633 helix: 0.80 (0.11), residues: 2145 sheet: -0.19 (0.19), residues: 675 loop : -1.06 (0.14), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 760 HIS 0.033 0.001 HIS M 811 PHE 0.031 0.002 PHE G 68 TYR 0.021 0.001 TYR H 86 ARG 0.008 0.000 ARG Y 250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 291 time to evaluate : 4.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8111 (mmt180) cc_final: 0.7565 (ttt180) REVERT: B 53 ARG cc_start: 0.7117 (ttm170) cc_final: 0.6807 (mtt90) REVERT: B 59 GLU cc_start: 0.8058 (pp20) cc_final: 0.7721 (pp20) REVERT: C 71 THR cc_start: 0.8740 (m) cc_final: 0.8494 (p) REVERT: C 77 LYS cc_start: 0.8192 (mmmm) cc_final: 0.7454 (mptt) REVERT: D 53 GLU cc_start: 0.7560 (tp30) cc_final: 0.6947 (mm-30) REVERT: D 59 LYS cc_start: 0.8778 (mmmt) cc_final: 0.8367 (pttp) REVERT: D 63 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7300 (tm-30) REVERT: D 92 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7163 (ptm160) REVERT: E 43 ARG cc_start: 0.6258 (tpp80) cc_final: 0.5991 (ttp-170) REVERT: E 72 ARG cc_start: 0.8278 (mmm160) cc_final: 0.7845 (mmm160) REVERT: E 76 LYS cc_start: 0.7589 (mttt) cc_final: 0.7170 (mmtp) REVERT: F 26 PHE cc_start: 0.7418 (m-80) cc_final: 0.6575 (m-80) REVERT: F 63 ILE cc_start: 0.6989 (mm) cc_final: 0.6777 (tp) REVERT: F 96 LYS cc_start: 0.6626 (tppt) cc_final: 0.6151 (mtmt) REVERT: F 102 THR cc_start: 0.8832 (m) cc_final: 0.8415 (p) REVERT: G 62 MET cc_start: 0.8173 (mmm) cc_final: 0.7972 (mmm) REVERT: G 89 LYS cc_start: 0.5757 (mttt) cc_final: 0.5097 (ptmm) REVERT: G 103 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7404 (pp) REVERT: H 39 THR cc_start: 0.5234 (t) cc_final: 0.4890 (p) REVERT: H 49 LYS cc_start: 0.6337 (mmmt) cc_final: 0.5942 (mttp) REVERT: H 95 ARG cc_start: 0.7943 (mmm160) cc_final: 0.7332 (mtt180) REVERT: M 762 MET cc_start: 0.7629 (ppp) cc_final: 0.7386 (ppp) REVERT: M 980 MET cc_start: 0.8009 (mmt) cc_final: 0.7567 (mmt) REVERT: M 1280 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7929 (tm-30) REVERT: M 1339 TYR cc_start: 0.7239 (OUTLIER) cc_final: 0.6271 (m-80) REVERT: R 238 MET cc_start: 0.8190 (mmm) cc_final: 0.7891 (mmm) REVERT: R 279 PHE cc_start: 0.6516 (OUTLIER) cc_final: 0.6213 (t80) REVERT: S 103 MET cc_start: 0.7448 (OUTLIER) cc_final: 0.7140 (mtp) REVERT: S 170 GLU cc_start: 0.7692 (tp30) cc_final: 0.7351 (tp30) REVERT: S 220 MET cc_start: 0.6852 (ttp) cc_final: 0.5892 (tpt) REVERT: T 278 THR cc_start: 0.8753 (OUTLIER) cc_final: 0.8329 (p) REVERT: U 164 ASP cc_start: 0.7645 (t70) cc_final: 0.7245 (t0) REVERT: U 283 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: W 86 MET cc_start: 0.8336 (tpt) cc_final: 0.7917 (tpp) REVERT: W 109 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8778 (tt) REVERT: W 175 MET cc_start: 0.8701 (mmm) cc_final: 0.8425 (tpp) REVERT: X 125 PHE cc_start: 0.8679 (OUTLIER) cc_final: 0.8227 (t80) REVERT: X 210 LYS cc_start: 0.8690 (tttt) cc_final: 0.8153 (tttt) REVERT: X 246 ASP cc_start: 0.7803 (OUTLIER) cc_final: 0.7351 (p0) REVERT: X 312 GLU cc_start: 0.8545 (OUTLIER) cc_final: 0.7682 (mp0) REVERT: Y 310 ASN cc_start: 0.7931 (m-40) cc_final: 0.7522 (m110) REVERT: Y 411 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7570 (mtp) outliers start: 177 outliers final: 151 residues processed: 442 average time/residue: 0.5400 time to fit residues: 394.7329 Evaluate side-chains 447 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 284 time to evaluate : 4.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain F residue 50 VAL Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 738 LEU Chi-restraints excluded: chain M residue 752 VAL Chi-restraints excluded: chain M residue 803 TYR Chi-restraints excluded: chain M residue 805 LEU Chi-restraints excluded: chain M residue 811 HIS Chi-restraints excluded: chain M residue 820 TYR Chi-restraints excluded: chain M residue 821 MET Chi-restraints excluded: chain M residue 832 PHE Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 867 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 978 ASN Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1006 THR Chi-restraints excluded: chain M residue 1007 SER Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1062 ILE Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1276 ASP Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1340 ASP Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 279 PHE Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 316 THR Chi-restraints excluded: chain R residue 400 MET Chi-restraints excluded: chain R residue 407 ASP Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 103 MET Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 179 TYR Chi-restraints excluded: chain S residue 182 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 263 ILE Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 135 GLU Chi-restraints excluded: chain T residue 154 ASN Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 135 LEU Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 283 GLU Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 301 LEU Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 386 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 189 ILE Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 228 GLU Chi-restraints excluded: chain V residue 252 LEU Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 303 LEU Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 402 LEU Chi-restraints excluded: chain V residue 417 GLN Chi-restraints excluded: chain V residue 436 VAL Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 135 LEU Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 196 SER Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 222 VAL Chi-restraints excluded: chain W residue 236 VAL Chi-restraints excluded: chain W residue 341 HIS Chi-restraints excluded: chain W residue 350 ARG Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 353 ILE Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 136 THR Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 246 ASP Chi-restraints excluded: chain X residue 278 THR Chi-restraints excluded: chain X residue 300 VAL Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 332 ILE Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 417 GLN Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 171 LEU Chi-restraints excluded: chain Y residue 220 ARG Chi-restraints excluded: chain Y residue 288 ILE Chi-restraints excluded: chain Y residue 313 LEU Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Y residue 437 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 442 optimal weight: 0.9980 chunk 466 optimal weight: 0.6980 chunk 425 optimal weight: 2.9990 chunk 453 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 356 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 chunk 409 optimal weight: 0.9980 chunk 428 optimal weight: 7.9990 chunk 451 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 42 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 422 HIS ** V 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 417 GLN ** X 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 44998 Z= 0.174 Angle : 0.581 11.137 62207 Z= 0.298 Chirality : 0.039 0.168 7288 Planarity : 0.003 0.053 6836 Dihedral : 22.567 155.354 8671 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 4.06 % Allowed : 18.09 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.02 (0.12), residues: 4633 helix: 0.94 (0.11), residues: 2150 sheet: -0.14 (0.20), residues: 678 loop : -0.98 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 760 HIS 0.005 0.001 HIS T 250 PHE 0.020 0.001 PHE R 120 TYR 0.018 0.001 TYR H 86 ARG 0.008 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 302 time to evaluate : 4.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8106 (mmt180) cc_final: 0.7581 (ttt180) REVERT: B 53 ARG cc_start: 0.7082 (ttm170) cc_final: 0.6828 (mtt90) REVERT: B 59 GLU cc_start: 0.8030 (pp20) cc_final: 0.7700 (pp20) REVERT: C 71 THR cc_start: 0.8752 (m) cc_final: 0.8515 (p) REVERT: C 77 LYS cc_start: 0.8187 (mmmm) cc_final: 0.7451 (mptt) REVERT: D 53 GLU cc_start: 0.7553 (tp30) cc_final: 0.6947 (mm-30) REVERT: D 59 LYS cc_start: 0.8721 (mmmt) cc_final: 0.8359 (pttp) REVERT: D 63 GLU cc_start: 0.7627 (tm-30) cc_final: 0.7266 (tm-30) REVERT: D 92 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.6868 (mtp85) REVERT: E 30 ARG cc_start: 0.8302 (mtt180) cc_final: 0.8076 (mtm180) REVERT: E 43 ARG cc_start: 0.6150 (tpp80) cc_final: 0.5928 (ttp-170) REVERT: E 72 ARG cc_start: 0.8254 (mmm160) cc_final: 0.7839 (mmm160) REVERT: E 93 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7784 (mm-30) REVERT: F 26 PHE cc_start: 0.7420 (m-80) cc_final: 0.6541 (m-80) REVERT: F 96 LYS cc_start: 0.6475 (tppt) cc_final: 0.6065 (mtmt) REVERT: F 102 THR cc_start: 0.8860 (m) cc_final: 0.8474 (p) REVERT: G 62 MET cc_start: 0.8193 (mmm) cc_final: 0.7962 (mmm) REVERT: G 89 LYS cc_start: 0.5795 (mttt) cc_final: 0.5129 (ptmm) REVERT: G 103 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7358 (pp) REVERT: H 39 THR cc_start: 0.5407 (t) cc_final: 0.4953 (p) REVERT: H 49 LYS cc_start: 0.6436 (mmmt) cc_final: 0.6116 (mttp) REVERT: H 95 ARG cc_start: 0.7974 (mmm160) cc_final: 0.7287 (mtt180) REVERT: M 762 MET cc_start: 0.7548 (ppp) cc_final: 0.7326 (ppp) REVERT: M 980 MET cc_start: 0.8028 (mmt) cc_final: 0.7577 (mmt) REVERT: M 1004 ILE cc_start: 0.7898 (mm) cc_final: 0.7579 (mm) REVERT: M 1280 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7945 (tm-30) REVERT: M 1339 TYR cc_start: 0.7230 (OUTLIER) cc_final: 0.6383 (m-80) REVERT: S 103 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.7094 (mtp) REVERT: S 170 GLU cc_start: 0.7733 (tp30) cc_final: 0.7448 (tp30) REVERT: S 220 MET cc_start: 0.6873 (ttp) cc_final: 0.5944 (tpt) REVERT: T 70 MET cc_start: 0.7724 (mmm) cc_final: 0.7360 (mmm) REVERT: T 278 THR cc_start: 0.8693 (OUTLIER) cc_final: 0.8291 (p) REVERT: T 326 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8549 (tppt) REVERT: U 164 ASP cc_start: 0.7633 (OUTLIER) cc_final: 0.7245 (t0) REVERT: U 175 MET cc_start: 0.8497 (tpp) cc_final: 0.8121 (tpp) REVERT: U 283 GLU cc_start: 0.7590 (OUTLIER) cc_final: 0.6856 (mp0) REVERT: W 86 MET cc_start: 0.8281 (tpt) cc_final: 0.7862 (tpp) REVERT: W 109 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8758 (tt) REVERT: W 175 MET cc_start: 0.8666 (mmm) cc_final: 0.8417 (tpp) REVERT: X 125 PHE cc_start: 0.8684 (OUTLIER) cc_final: 0.8350 (t80) REVERT: X 210 LYS cc_start: 0.8678 (tttt) cc_final: 0.8144 (tttt) REVERT: X 246 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7348 (p0) REVERT: X 312 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7903 (mt-10) REVERT: Y 411 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7529 (mtp) outliers start: 162 outliers final: 131 residues processed: 441 average time/residue: 0.5556 time to fit residues: 407.2588 Evaluate side-chains 433 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 288 time to evaluate : 4.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain G residue 51 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 738 LEU Chi-restraints excluded: chain M residue 752 VAL Chi-restraints excluded: chain M residue 803 TYR Chi-restraints excluded: chain M residue 805 LEU Chi-restraints excluded: chain M residue 820 TYR Chi-restraints excluded: chain M residue 821 MET Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 867 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1006 THR Chi-restraints excluded: chain M residue 1007 SER Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1062 ILE Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1276 ASP Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1340 ASP Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 316 THR Chi-restraints excluded: chain R residue 400 MET Chi-restraints excluded: chain R residue 407 ASP Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 103 MET Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 179 TYR Chi-restraints excluded: chain S residue 182 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 263 ILE Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 88 LEU Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 135 GLU Chi-restraints excluded: chain T residue 154 ASN Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 135 LEU Chi-restraints excluded: chain U residue 141 VAL Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 164 ASP Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 283 GLU Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 386 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 402 LEU Chi-restraints excluded: chain V residue 436 VAL Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 222 VAL Chi-restraints excluded: chain W residue 341 HIS Chi-restraints excluded: chain W residue 350 ARG Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 353 ILE Chi-restraints excluded: chain W residue 384 LEU Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 136 THR Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 246 ASP Chi-restraints excluded: chain X residue 300 VAL Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 332 ILE Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 378 ASP Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 417 GLN Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 171 LEU Chi-restraints excluded: chain Y residue 220 ARG Chi-restraints excluded: chain Y residue 257 LEU Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Y residue 437 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 297 optimal weight: 2.9990 chunk 479 optimal weight: 0.8980 chunk 292 optimal weight: 1.9990 chunk 227 optimal weight: 5.9990 chunk 333 optimal weight: 0.0370 chunk 503 optimal weight: 0.2980 chunk 463 optimal weight: 0.5980 chunk 400 optimal weight: 1.9990 chunk 41 optimal weight: 5.9990 chunk 309 optimal weight: 3.9990 chunk 245 optimal weight: 5.9990 overall best weight: 0.7660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 42 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 808 GLN ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 44998 Z= 0.168 Angle : 0.578 11.334 62207 Z= 0.295 Chirality : 0.039 0.168 7288 Planarity : 0.003 0.051 6836 Dihedral : 22.513 155.547 8669 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.17 % Favored : 95.81 % Rotamer: Outliers : 3.66 % Allowed : 18.64 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.10 (0.12), residues: 4633 helix: 1.01 (0.12), residues: 2150 sheet: -0.10 (0.19), residues: 701 loop : -0.97 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 760 HIS 0.005 0.001 HIS T 250 PHE 0.034 0.001 PHE G 68 TYR 0.017 0.001 TYR H 86 ARG 0.011 0.000 ARG F 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 303 time to evaluate : 4.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8100 (mmt180) cc_final: 0.7579 (ttt180) REVERT: A 99 TYR cc_start: 0.6783 (t80) cc_final: 0.6454 (t80) REVERT: B 53 ARG cc_start: 0.7083 (ttm170) cc_final: 0.6833 (mtt90) REVERT: B 59 GLU cc_start: 0.8016 (pp20) cc_final: 0.7649 (pp20) REVERT: C 77 LYS cc_start: 0.8194 (mmmm) cc_final: 0.7499 (mptt) REVERT: D 53 GLU cc_start: 0.7536 (tp30) cc_final: 0.6936 (mm-30) REVERT: D 59 LYS cc_start: 0.8718 (mmmt) cc_final: 0.8371 (pttp) REVERT: D 92 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.6839 (mtp85) REVERT: E 30 ARG cc_start: 0.8297 (mtt180) cc_final: 0.8089 (mtm180) REVERT: E 43 ARG cc_start: 0.6140 (tpp80) cc_final: 0.5927 (ttp-170) REVERT: E 72 ARG cc_start: 0.8245 (mmm160) cc_final: 0.7831 (mmm160) REVERT: E 93 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7799 (mm-30) REVERT: F 26 PHE cc_start: 0.7407 (m-80) cc_final: 0.6563 (m-80) REVERT: F 96 LYS cc_start: 0.6529 (tppt) cc_final: 0.6104 (mtmt) REVERT: F 102 THR cc_start: 0.8918 (m) cc_final: 0.8550 (p) REVERT: G 62 MET cc_start: 0.8162 (mmm) cc_final: 0.7943 (mmm) REVERT: G 89 LYS cc_start: 0.5916 (mttt) cc_final: 0.5186 (ptmm) REVERT: G 103 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7360 (pp) REVERT: H 39 THR cc_start: 0.5371 (t) cc_final: 0.4941 (p) REVERT: H 49 LYS cc_start: 0.6467 (mmmt) cc_final: 0.6152 (mttp) REVERT: H 95 ARG cc_start: 0.8039 (mmm160) cc_final: 0.7380 (mtt180) REVERT: M 762 MET cc_start: 0.7541 (ppp) cc_final: 0.7319 (ppp) REVERT: M 980 MET cc_start: 0.8003 (mmt) cc_final: 0.7532 (mmt) REVERT: M 1004 ILE cc_start: 0.7832 (mm) cc_final: 0.7515 (mm) REVERT: M 1280 GLN cc_start: 0.8243 (tm-30) cc_final: 0.7964 (tm-30) REVERT: M 1339 TYR cc_start: 0.7190 (OUTLIER) cc_final: 0.6332 (m-80) REVERT: R 238 MET cc_start: 0.8141 (mmm) cc_final: 0.7907 (mmm) REVERT: S 170 GLU cc_start: 0.7721 (tp30) cc_final: 0.7427 (tp30) REVERT: S 220 MET cc_start: 0.6869 (ttp) cc_final: 0.5937 (tpt) REVERT: T 70 MET cc_start: 0.7688 (mmm) cc_final: 0.7329 (mmm) REVERT: T 278 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.8340 (p) REVERT: T 326 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8550 (tppt) REVERT: U 175 MET cc_start: 0.8479 (tpp) cc_final: 0.8123 (tpp) REVERT: U 283 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: W 86 MET cc_start: 0.8277 (tpt) cc_final: 0.7847 (tpp) REVERT: W 109 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8776 (tt) REVERT: W 175 MET cc_start: 0.8656 (mmm) cc_final: 0.8408 (tpp) REVERT: X 125 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.8335 (t80) REVERT: X 210 LYS cc_start: 0.8756 (tttt) cc_final: 0.8200 (tttt) REVERT: X 312 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7875 (mt-10) REVERT: Y 115 GLU cc_start: 0.7939 (tm-30) cc_final: 0.7575 (tm-30) REVERT: Y 310 ASN cc_start: 0.7820 (m-40) cc_final: 0.7410 (m110) REVERT: Y 411 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7530 (mtp) outliers start: 146 outliers final: 124 residues processed: 426 average time/residue: 0.5526 time to fit residues: 388.0618 Evaluate side-chains 425 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 290 time to evaluate : 4.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 92 ARG Chi-restraints excluded: chain E residue 93 GLU Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain F residue 42 GLN Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain H residue 64 ILE Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 738 LEU Chi-restraints excluded: chain M residue 752 VAL Chi-restraints excluded: chain M residue 803 TYR Chi-restraints excluded: chain M residue 805 LEU Chi-restraints excluded: chain M residue 820 TYR Chi-restraints excluded: chain M residue 821 MET Chi-restraints excluded: chain M residue 860 LEU Chi-restraints excluded: chain M residue 867 LEU Chi-restraints excluded: chain M residue 962 ASP Chi-restraints excluded: chain M residue 978 ASN Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1006 THR Chi-restraints excluded: chain M residue 1007 SER Chi-restraints excluded: chain M residue 1010 LEU Chi-restraints excluded: chain M residue 1052 LYS Chi-restraints excluded: chain M residue 1062 ILE Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1276 ASP Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1340 ASP Chi-restraints excluded: chain M residue 1380 LEU Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 15 ILE Chi-restraints excluded: chain R residue 39 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 128 LEU Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 244 LEU Chi-restraints excluded: chain R residue 253 LEU Chi-restraints excluded: chain R residue 266 THR Chi-restraints excluded: chain R residue 295 VAL Chi-restraints excluded: chain R residue 316 THR Chi-restraints excluded: chain R residue 400 MET Chi-restraints excluded: chain S residue 17 ILE Chi-restraints excluded: chain S residue 49 ILE Chi-restraints excluded: chain S residue 116 VAL Chi-restraints excluded: chain S residue 179 TYR Chi-restraints excluded: chain S residue 182 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 263 ILE Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 125 PHE Chi-restraints excluded: chain T residue 135 GLU Chi-restraints excluded: chain T residue 154 ASN Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain T residue 278 THR Chi-restraints excluded: chain T residue 326 LYS Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 355 SER Chi-restraints excluded: chain T residue 462 TYR Chi-restraints excluded: chain U residue 19 LEU Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 135 LEU Chi-restraints excluded: chain U residue 158 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 283 GLU Chi-restraints excluded: chain U residue 298 VAL Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 341 HIS Chi-restraints excluded: chain U residue 352 ILE Chi-restraints excluded: chain U residue 386 LEU Chi-restraints excluded: chain U residue 403 ILE Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain V residue 121 LEU Chi-restraints excluded: chain V residue 139 VAL Chi-restraints excluded: chain V residue 162 THR Chi-restraints excluded: chain V residue 168 VAL Chi-restraints excluded: chain V residue 194 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 336 VAL Chi-restraints excluded: chain V residue 337 VAL Chi-restraints excluded: chain V residue 364 ILE Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 402 LEU Chi-restraints excluded: chain V residue 436 VAL Chi-restraints excluded: chain V residue 461 ASN Chi-restraints excluded: chain W residue 26 ILE Chi-restraints excluded: chain W residue 71 VAL Chi-restraints excluded: chain W residue 101 ILE Chi-restraints excluded: chain W residue 109 LEU Chi-restraints excluded: chain W residue 125 ILE Chi-restraints excluded: chain W residue 149 ILE Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 200 THR Chi-restraints excluded: chain W residue 222 VAL Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 396 LEU Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 92 ILE Chi-restraints excluded: chain X residue 121 LEU Chi-restraints excluded: chain X residue 125 PHE Chi-restraints excluded: chain X residue 136 THR Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 194 VAL Chi-restraints excluded: chain X residue 209 VAL Chi-restraints excluded: chain X residue 246 ASP Chi-restraints excluded: chain X residue 300 VAL Chi-restraints excluded: chain X residue 312 GLU Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 332 ILE Chi-restraints excluded: chain X residue 336 VAL Chi-restraints excluded: chain X residue 378 ASP Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 417 GLN Chi-restraints excluded: chain X residue 428 THR Chi-restraints excluded: chain Y residue 23 HIS Chi-restraints excluded: chain Y residue 32 ASP Chi-restraints excluded: chain Y residue 171 LEU Chi-restraints excluded: chain Y residue 220 ARG Chi-restraints excluded: chain Y residue 257 LEU Chi-restraints excluded: chain Y residue 352 ILE Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Y residue 437 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 505 random chunks: chunk 318 optimal weight: 1.9990 chunk 426 optimal weight: 0.0470 chunk 122 optimal weight: 5.9990 chunk 369 optimal weight: 0.7980 chunk 59 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 401 optimal weight: 0.9990 chunk 167 optimal weight: 0.1980 chunk 412 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 73 optimal weight: 0.4980 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 42 GLN ** F 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 827 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 417 GLN W 63 ASN ** X 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.119987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.091056 restraints weight = 109566.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.090720 restraints weight = 97153.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.090803 restraints weight = 75252.448| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 44998 Z= 0.154 Angle : 0.569 10.890 62207 Z= 0.291 Chirality : 0.038 0.170 7288 Planarity : 0.003 0.051 6836 Dihedral : 22.463 155.604 8669 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.01 % Favored : 95.96 % Rotamer: Outliers : 3.53 % Allowed : 18.66 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.19 (0.12), residues: 4633 helix: 1.07 (0.12), residues: 2159 sheet: 0.01 (0.20), residues: 693 loop : -0.94 (0.14), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 760 HIS 0.005 0.001 HIS C 75 PHE 0.029 0.001 PHE G 68 TYR 0.034 0.001 TYR R 419 ARG 0.009 0.000 ARG A 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9285.49 seconds wall clock time: 174 minutes 22.45 seconds (10462.45 seconds total)