Starting phenix.real_space_refine on Mon Mar 25 01:13:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gen_4396/03_2024/6gen_4396_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gen_4396/03_2024/6gen_4396.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/6gen_4396/03_2024/6gen_4396.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gen_4396/03_2024/6gen_4396.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gen_4396/03_2024/6gen_4396_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gen_4396/03_2024/6gen_4396_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= 0.007 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 362 5.49 5 Mg 8 5.21 5 S 118 5.16 5 Be 2 3.05 5 C 26898 2.51 5 N 7881 2.21 5 O 9204 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 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 ARG 1133": "NH1" <-> "NH2" Residue "M ASP 1159": "OD1" <-> "OD2" Residue "M ARG 1291": "NH1" <-> "NH2" Residue "M ARG 1313": "NH1" <-> "NH2" Residue "M ARG 1357": "NH1" <-> "NH2" 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 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 TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 286": "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 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 GLU 37": "OE1" <-> "OE2" Residue "T TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 191": "NH1" <-> "NH2" Residue "T ARG 258": "NH1" <-> "NH2" Residue "T ARG 348": "NH1" <-> "NH2" Residue "T ARG 392": "NH1" <-> "NH2" Residue "T ARG 413": "NH1" <-> "NH2" Residue "T GLU 441": "OE1" <-> "OE2" Residue "T TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 52": "NH1" <-> "NH2" Residue "U ARG 69": "NH1" <-> "NH2" Residue "U ARG 122": "NH1" <-> "NH2" Residue "U TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 204": "NH1" <-> "NH2" Residue "U PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 266": "NH1" <-> "NH2" Residue "U ARG 311": "NH1" <-> "NH2" Residue "U ARG 333": "NH1" <-> "NH2" Residue "U ASP 349": "OD1" <-> "OD2" Residue "U ARG 397": "NH1" <-> "NH2" Residue "U ARG 413": "NH1" <-> "NH2" Residue "U GLU 421": "OE1" <-> "OE2" Residue "U ARG 425": "NH1" <-> "NH2" Residue "U ARG 435": "NH1" <-> "NH2" Residue "U TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 23": "NH1" <-> "NH2" Residue "V GLU 37": "OE1" <-> "OE2" Residue "V ARG 191": "NH1" <-> "NH2" Residue "V ARG 258": "NH1" <-> "NH2" Residue "V ARG 348": "NH1" <-> "NH2" Residue "V ARG 392": "NH1" <-> "NH2" Residue "V ARG 413": "NH1" <-> "NH2" Residue "V GLU 441": "OE1" <-> "OE2" Residue "V TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 52": "NH1" <-> "NH2" Residue "W ARG 69": "NH1" <-> "NH2" Residue "W ARG 122": "NH1" <-> "NH2" Residue "W TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 204": "NH1" <-> "NH2" Residue "W PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ASP 349": "OD1" <-> "OD2" 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 TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 191": "NH1" <-> "NH2" Residue "X ARG 258": "NH1" <-> "NH2" Residue "X ARG 348": "NH1" <-> "NH2" Residue "X ARG 392": "NH1" <-> "NH2" Residue "X ARG 413": "NH1" <-> "NH2" Residue "X GLU 441": "OE1" <-> "OE2" Residue "X TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Y ARG 69": "NH1" <-> "NH2" 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 PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 266": "NH1" <-> "NH2" Residue "Y ARG 311": "NH1" <-> "NH2" Residue "Y ARG 333": "NH1" <-> "NH2" Residue "Y ASP 349": "OD1" <-> "OD2" Residue "Y ARG 397": "NH1" <-> "NH2" Residue "Y ARG 413": "NH1" <-> "NH2" Residue "Y GLU 421": "OE1" <-> "OE2" Residue "Y ARG 425": "NH1" <-> "NH2" Residue "Y ARG 435": "NH1" <-> "NH2" Residue "Y TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 44481 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: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 3525 Classifications: {'DNA': 173} Link IDs: {'rna3p': 172} Chain: "J" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 3568 Classifications: {'DNA': 173} Link IDs: {'rna3p': 172} 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: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23819 SG CYS S 244 49.911 70.845 117.679 1.00 74.04 S ATOM 23839 SG CYS S 247 46.584 68.555 114.591 1.00 61.50 S ATOM 23955 SG CYS S 264 47.615 71.995 114.554 1.00 90.14 S ATOM 23980 SG CYS S 268 45.500 71.489 117.455 1.00 85.21 S ATOM 23899 SG CYS S 256 52.142 78.661 124.394 1.00 96.12 S ATOM 23920 SG CYS S 259 53.977 75.901 126.523 1.00 80.86 S ATOM 24059 SG CYS S 277 50.955 77.008 128.993 1.00111.59 S Time building chain proxies: 21.35, per 1000 atoms: 0.48 Number of scatterers: 44481 At special positions: 0 Unit cell: (169.83, 199.8, 206.46, 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 362 15.00 Mg 8 11.99 F 6 9.00 O 9204 8.00 N 7881 7.00 C 26898 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: 22.05 Conformation dependent library (CDL) restraints added in 7.6 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 244 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 268 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 247 " pdb=" ZN S 502 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 259 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 277 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 256 " pdb="ZN ZN S 502 " - pdb=" NE2 HIS S 272 " 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: 195 helices and 34 sheets defined 42.6% alpha, 10.3% beta 167 base pairs and 294 stacking pairs defined. Time for finding SS restraints: 24.44 Creating SS restraints... Processing helix chain 'Z' and resid 102 through 128 Processing helix chain 'Z' and resid 137 through 141 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 90 through 113 Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 64 through 74 Processing helix chain 'B' and resid 90 through 113 Processing helix chain 'B' and resid 121 through 129 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: 3.518A pdb=" N GLU C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP C 68 " --> pdb=" O SER C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 89 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: 3.517A pdb=" N GLU D 63 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP D 68 " --> pdb=" O SER D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 89 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 36 Processing helix chain 'E' and resid 48 through 73 Processing helix chain 'E' and resid 81 through 89 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 36 Processing helix chain 'F' and resid 48 through 73 Processing helix chain 'F' and resid 81 through 89 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: 3.636A 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: 3.636A 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: 4.083A pdb=" N SER M 709 " --> pdb=" O ASN M 705 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU M 710 " --> pdb=" O TRP M 706 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N TYR M 711 " --> pdb=" O LEU M 707 " (cutoff:3.500A) Processing helix chain 'M' and resid 727 through 741 removed outlier: 3.517A pdb=" N ALA M 739 " --> pdb=" O LEU M 735 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N CYS M 740 " --> pdb=" O ALA M 736 " (cutoff:3.500A) Processing helix chain 'M' and resid 757 through 766 removed outlier: 3.955A pdb=" N GLU M 761 " --> pdb=" O LEU M 757 " (cutoff:3.500A) Processing helix chain 'M' and resid 782 through 788 Processing helix chain 'M' and resid 805 through 808 No H-bonds generated for 'chain 'M' and resid 805 through 808' Processing helix chain 'M' and resid 810 through 813 No H-bonds generated for 'chain 'M' and resid 810 through 813' 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: 3.853A pdb=" N HIS M 922 " --> pdb=" O VAL M 918 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN M 923 " --> pdb=" O ALA M 919 " (cutoff:3.500A) removed outlier: 3.928A 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 980 through 993 removed outlier: 4.665A pdb=" N GLN M 988 " --> pdb=" O ASN M 984 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU M 989 " --> pdb=" O CYS M 985 " (cutoff:3.500A) Processing helix chain 'M' and resid 1014 through 1029 removed outlier: 3.753A pdb=" N TYR M1018 " --> pdb=" O VAL M1014 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ASP M1020 " --> pdb=" O SER M1016 " (cutoff:3.500A) removed outlier: 5.047A 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 1063 Processing helix chain 'M' and resid 1071 through 1093 removed outlier: 3.602A pdb=" N LEU M1078 " --> pdb=" O GLU M1074 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU M1080 " --> pdb=" O ASN M1076 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR M1081 " --> pdb=" O LYS M1077 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU M1085 " --> pdb=" O THR M1081 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU M1088 " --> pdb=" O GLN M1084 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N GLU M1091 " --> pdb=" O GLU M1087 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ALA M1092 " --> pdb=" O GLU M1088 " (cutoff:3.500A) Processing helix chain 'M' and resid 1105 through 1133 removed outlier: 3.901A pdb=" N ASP M1117 " --> pdb=" O GLU M1113 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N MET M1118 " --> pdb=" O GLY M1114 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU M1122 " --> pdb=" O MET M1118 " (cutoff:3.500A) removed outlier: 3.886A 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 1166 through 1172 removed outlier: 3.738A 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 1193 through 1197 removed outlier: 4.061A pdb=" N LEU M1197 " --> pdb=" O ARG M1193 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1193 through 1197' Processing helix chain 'M' and resid 1209 through 1219 Processing helix chain 'M' and resid 1225 through 1232 Processing helix chain 'M' and resid 1238 through 1243 removed outlier: 4.013A pdb=" N LEU M1241 " --> pdb=" O LYS M1238 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN M1242 " --> pdb=" O SER M1239 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR M1243 " --> pdb=" O LEU M1240 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 1238 through 1243' Processing helix chain 'M' and resid 1251 through 1260 Processing helix chain 'M' and resid 1272 through 1285 removed outlier: 4.370A pdb=" N ASP M1276 " --> pdb=" O LYS M1273 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL M1277 " --> pdb=" O VAL M1274 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE M1281 " --> pdb=" O LEU M1278 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU M1282 " --> pdb=" O GLU M1279 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN M1283 " --> pdb=" O GLN M1280 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N HIS M1285 " --> pdb=" O LEU M1282 " (cutoff:3.500A) Processing helix chain 'M' and resid 1299 through 1309 removed outlier: 3.982A pdb=" N ILE M1303 " --> pdb=" O GLU M1299 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE M1308 " --> pdb=" O LEU M1304 " (cutoff:3.500A) Processing helix chain 'M' and resid 1347 through 1355 removed outlier: 3.762A pdb=" N CYS M1351 " --> pdb=" O MET M1347 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N CYS M1355 " --> pdb=" O CYS M1351 " (cutoff:3.500A) Processing helix chain 'M' and resid 1375 through 1385 removed outlier: 3.801A pdb=" N LEU M1380 " --> pdb=" O GLU M1376 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS M1381 " --> pdb=" O SER M1377 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN M1385 " --> pdb=" O LYS M1381 " (cutoff:3.500A) Processing helix chain 'R' and resid 69 through 80 Processing helix chain 'R' and resid 109 through 121 Processing helix chain 'R' and resid 133 through 142 removed outlier: 3.663A pdb=" N VAL R 137 " --> pdb=" O VAL R 133 " (cutoff:3.500A) Proline residue: R 138 - end of helix removed outlier: 5.228A pdb=" N LYS R 141 " --> pdb=" O VAL R 137 " (cutoff:3.500A) removed outlier: 5.312A 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 243 through 251 Processing helix chain 'R' and resid 260 through 265 Processing helix chain 'R' and resid 308 through 316 removed outlier: 3.969A pdb=" N ILE R 313 " --> pdb=" O GLU R 309 " (cutoff:3.500A) Proline residue: R 314 - end of helix 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 374 Processing helix chain 'R' and resid 392 through 402 Processing helix chain 'R' and resid 407 through 412 Processing helix chain 'R' and resid 416 through 421 Processing helix chain 'R' and resid 424 through 429 removed outlier: 4.189A pdb=" N THR R 428 " --> pdb=" O PRO R 424 " (cutoff:3.500A) Processing helix chain 'R' and resid 434 through 437 No H-bonds generated for 'chain 'R' and resid 434 through 437' 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: 4.670A 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 226 Processing helix chain 'S' and resid 266 through 270 Processing helix chain 'T' and resid 52 through 66 Processing helix chain 'T' and resid 86 through 96 Processing helix chain 'T' and resid 107 through 110 removed outlier: 3.622A pdb=" N LEU T 110 " --> pdb=" O GLY T 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 107 through 110' Processing helix chain 'T' and resid 117 through 127 Processing helix chain 'T' and resid 183 through 191 Processing helix chain 'T' and resid 216 through 218 No H-bonds generated for 'chain 'T' and resid 216 through 218' Processing helix chain 'T' and resid 249 through 257 Processing helix chain 'T' and resid 265 through 273 Processing helix chain 'T' and resid 282 through 297 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: 3.578A 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 365 Processing helix chain 'T' and resid 377 through 390 Processing helix chain 'T' and resid 397 through 407 Processing helix chain 'T' and resid 412 through 417 Processing helix chain 'T' and resid 419 through 428 removed outlier: 3.742A pdb=" N GLY T 423 " --> pdb=" O LEU T 419 " (cutoff:3.500A) Processing helix chain 'T' and resid 436 through 445 Processing helix chain 'T' and resid 449 through 457 Processing helix chain 'U' and resid 48 through 63 Processing helix chain 'U' and resid 81 through 92 Processing helix chain 'U' and resid 113 through 123 Processing helix chain 'U' and resid 173 through 181 Processing helix chain 'U' and resid 241 through 249 Processing helix chain 'U' and resid 251 through 253 No H-bonds generated for 'chain 'U' and resid 251 through 253' Processing helix chain 'U' and resid 255 through 259 Processing helix chain 'U' and resid 267 through 283 Processing helix chain 'U' and resid 303 through 314 removed outlier: 4.986A pdb=" N GLU U 314 " --> pdb=" O ASN U 310 " (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 349 Processing helix chain 'U' and resid 361 through 374 removed outlier: 3.541A pdb=" N LYS U 365 " --> pdb=" O GLU U 361 " (cutoff:3.500A) Processing helix chain 'U' and resid 381 through 393 Processing helix chain 'U' and resid 396 through 412 removed outlier: 4.459A pdb=" N SER U 404 " --> pdb=" O SER U 400 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLN U 407 " --> pdb=" O ILE U 403 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN U 408 " --> pdb=" O SER U 404 " (cutoff:3.500A) Processing helix chain 'U' and resid 420 through 429 Processing helix chain 'U' and resid 433 through 442 Processing helix chain 'V' and resid 52 through 66 Processing helix chain 'V' and resid 86 through 96 Processing helix chain 'V' and resid 107 through 110 removed outlier: 3.622A 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 Processing helix chain 'V' and resid 183 through 191 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 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 328 removed outlier: 3.579A 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 Processing helix chain 'V' and resid 377 through 390 Processing helix chain 'V' and resid 397 through 407 Processing helix chain 'V' and resid 412 through 417 Processing helix chain 'V' and resid 419 through 428 removed outlier: 3.742A pdb=" N GLY V 423 " --> pdb=" O LEU V 419 " (cutoff:3.500A) 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 Processing helix chain 'W' and resid 81 through 92 Processing helix chain 'W' and resid 113 through 123 Processing helix chain 'W' and resid 173 through 181 Processing helix chain 'W' and resid 241 through 249 Processing helix chain 'W' and resid 251 through 253 No H-bonds generated for 'chain 'W' and resid 251 through 253' Processing helix chain 'W' and resid 255 through 259 Processing helix chain 'W' and resid 267 through 283 Processing helix chain 'W' and resid 303 through 314 removed outlier: 4.987A 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 349 Processing helix chain 'W' and resid 361 through 374 removed outlier: 3.541A 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 412 removed outlier: 4.459A pdb=" N SER W 404 " --> pdb=" O SER W 400 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN W 407 " --> pdb=" O ILE W 403 " (cutoff:3.500A) removed outlier: 3.889A 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 Processing helix chain 'X' and resid 52 through 66 Processing helix chain 'X' and resid 86 through 96 Processing helix chain 'X' and resid 107 through 110 removed outlier: 3.623A 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 127 Processing helix chain 'X' and resid 183 through 191 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 Processing helix chain 'X' and resid 265 through 273 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 328 removed outlier: 3.578A 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 365 Processing helix chain 'X' and resid 377 through 390 Processing helix chain 'X' and resid 397 through 407 Processing helix chain 'X' and resid 412 through 417 Processing helix chain 'X' and resid 419 through 428 removed outlier: 3.743A pdb=" N GLY X 423 " --> pdb=" O LEU X 419 " (cutoff:3.500A) Processing helix chain 'X' and resid 436 through 445 Processing helix chain 'X' and resid 449 through 457 Processing helix chain 'Y' and resid 48 through 63 Processing helix chain 'Y' and resid 81 through 92 Processing helix chain 'Y' and resid 113 through 123 Processing helix chain 'Y' and resid 173 through 180 Processing helix chain 'Y' and resid 241 through 249 Processing helix chain 'Y' and resid 251 through 253 No H-bonds generated for 'chain 'Y' and resid 251 through 253' Processing helix chain 'Y' and resid 255 through 259 Processing helix chain 'Y' and resid 267 through 283 Processing helix chain 'Y' and resid 303 through 314 removed outlier: 4.987A 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 374 removed outlier: 3.542A pdb=" N LYS Y 365 " --> pdb=" O GLU Y 361 " (cutoff:3.500A) Processing helix chain 'Y' and resid 381 through 393 Processing helix chain 'Y' and resid 396 through 412 removed outlier: 4.459A pdb=" N SER Y 404 " --> pdb=" O SER Y 400 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN Y 407 " --> pdb=" O ILE Y 403 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLN Y 408 " --> pdb=" O SER Y 404 " (cutoff:3.500A) Processing helix chain 'Y' and resid 420 through 429 Processing helix chain 'Y' and resid 433 through 442 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 798 through 802 removed outlier: 6.709A pdb=" N HIS M 748 " --> pdb=" O CYS M 799 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N VAL M 801 " --> pdb=" O HIS M 748 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ILE M 750 " --> pdb=" O VAL M 801 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N ARG M 847 " --> pdb=" O MET M 821 " (cutoff:3.500A) removed outlier: 8.838A pdb=" N LEU M 823 " --> pdb=" O ARG M 847 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU M 849 " --> pdb=" O LEU M 823 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'M' and resid 944 through 946 removed outlier: 6.694A pdb=" N VAL M1364 " --> pdb=" O TYR M 945 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'M' and resid 949 through 951 Processing sheet with id= E, first strand: chain 'M' and resid 1335 through 1338 removed outlier: 4.092A pdb=" N THR M1269 " --> pdb=" O LEU M1319 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET M1290 " --> pdb=" O VAL M1316 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'R' and resid 6 through 9 removed outlier: 3.529A pdb=" N ALA R 28 " --> pdb=" O ILE R 15 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE R 17 " --> pdb=" O PHE R 26 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'R' and resid 32 through 35 Processing sheet with id= H, first strand: chain 'R' and resid 98 through 101 removed outlier: 6.759A pdb=" N SER R 127 " --> pdb=" O LEU R 99 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ALA R 101 " --> pdb=" O SER R 127 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N PHE R 129 " --> pdb=" O ALA R 101 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'R' and resid 147 through 151 removed outlier: 5.965A pdb=" N ILE R 353 " --> pdb=" O SER R 386 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N CYS R 355 " --> pdb=" O PRO R 388 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N LEU R 189 " --> pdb=" O VAL R 354 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N THR R 356 " --> pdb=" O LEU R 189 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE R 191 " --> pdb=" O THR R 356 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'R' and resid 286 through 289 removed outlier: 4.084A pdb=" N TYR R 286 " --> pdb=" O VAL R 275 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL R 275 " --> pdb=" O TYR R 286 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'T' and resid 367 through 371 removed outlier: 7.168A pdb=" N ALA T 74 " --> pdb=" O LEU T 368 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N VAL T 370 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N LEU T 76 " --> pdb=" O VAL T 370 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N VAL T 336 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N LEU T 77 " --> pdb=" O VAL T 336 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU T 338 " --> pdb=" O LEU T 77 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU T 308 " --> pdb=" O VAL T 335 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'T' and resid 130 through 132 removed outlier: 3.690A pdb=" N ARG T 132 " --> pdb=" O GLU T 302 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU T 302 " --> pdb=" O ARG T 132 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'T' and resid 238 through 243 removed outlier: 3.799A pdb=" N LYS T 241 " --> pdb=" O LYS T 137 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS T 137 " --> pdb=" O LYS T 241 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU T 135 " --> pdb=" O ILE T 243 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY T 142 " --> pdb=" O ILE T 200 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR T 201 " --> pdb=" O ARG T 211 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG T 211 " --> pdb=" O TYR T 201 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLU T 203 " --> pdb=" O VAL T 209 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL T 209 " --> pdb=" O GLU T 203 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'T' and resid 166 through 171 removed outlier: 4.520A pdb=" N VAL T 166 " --> pdb=" O LEU T 181 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU T 181 " --> pdb=" O VAL T 166 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'U' and resid 351 through 356 removed outlier: 7.057A pdb=" N ALA U 70 " --> pdb=" O ILE U 352 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ILE U 354 " --> pdb=" O ALA U 70 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU U 72 " --> pdb=" O ILE U 354 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N THR U 356 " --> pdb=" O LEU U 72 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ALA U 74 " --> pdb=" O THR U 356 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL U 321 " --> pdb=" O VAL U 71 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL U 73 " --> pdb=" O VAL U 321 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N MET U 323 " --> pdb=" O VAL U 73 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N GLY U 75 " --> pdb=" O MET U 323 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'U' and resid 230 through 240 Processing sheet with id= Q, first strand: chain 'U' and resid 135 through 138 removed outlier: 3.616A pdb=" N GLY U 138 " --> pdb=" O ILE U 190 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE U 190 " --> pdb=" O GLY U 138 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY U 203 " --> pdb=" O VAL U 189 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER U 191 " --> pdb=" O LYS U 201 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LYS U 201 " --> pdb=" O SER U 191 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASP U 193 " --> pdb=" O ILE U 199 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE U 199 " --> pdb=" O ASP U 193 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'U' and resid 143 through 146 removed outlier: 3.713A pdb=" N GLY U 156 " --> pdb=" O LEU U 171 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'V' and resid 367 through 371 removed outlier: 7.168A pdb=" N ALA V 74 " --> pdb=" O LEU V 368 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL V 370 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N LEU V 76 " --> pdb=" O VAL V 370 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL V 336 " --> pdb=" O ILE V 75 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU V 77 " --> pdb=" O VAL V 336 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU V 338 " --> pdb=" O LEU V 77 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU V 308 " --> pdb=" O VAL V 335 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'V' and resid 130 through 132 removed outlier: 3.689A pdb=" N ARG V 132 " --> pdb=" O GLU V 302 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU V 302 " --> pdb=" O ARG V 132 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'V' and resid 238 through 243 removed outlier: 3.798A pdb=" N LYS V 241 " --> pdb=" O LYS V 137 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS V 137 " --> pdb=" O LYS V 241 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU V 135 " --> pdb=" O ILE V 243 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY V 142 " --> pdb=" O ILE V 200 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR V 201 " --> pdb=" O ARG V 211 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG V 211 " --> pdb=" O TYR V 201 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N GLU V 203 " --> pdb=" O VAL V 209 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL V 209 " --> pdb=" O GLU V 203 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'V' and resid 166 through 171 removed outlier: 4.520A pdb=" N VAL V 166 " --> pdb=" O LEU V 181 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU V 181 " --> pdb=" O VAL V 166 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'W' and resid 351 through 356 removed outlier: 7.057A pdb=" N ALA W 70 " --> pdb=" O ILE W 352 " (cutoff:3.500A) removed outlier: 8.379A pdb=" N ILE W 354 " --> pdb=" O ALA W 70 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU W 72 " --> pdb=" O ILE W 354 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N THR W 356 " --> pdb=" O LEU W 72 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA W 74 " --> pdb=" O THR W 356 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N VAL W 321 " --> pdb=" O VAL W 71 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL W 73 " --> pdb=" O VAL W 321 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N MET W 323 " --> pdb=" O VAL W 73 " (cutoff:3.500A) removed outlier: 8.388A pdb=" N GLY W 75 " --> pdb=" O MET W 323 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'W' and resid 230 through 240 Processing sheet with id= Y, first strand: chain 'W' and resid 135 through 138 removed outlier: 3.617A pdb=" N GLY W 138 " --> pdb=" O ILE W 190 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE W 190 " --> pdb=" O GLY W 138 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY W 203 " --> pdb=" O VAL W 189 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N SER W 191 " --> pdb=" O LYS W 201 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LYS W 201 " --> pdb=" O SER W 191 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASP W 193 " --> pdb=" O ILE W 199 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N ILE W 199 " --> pdb=" O ASP W 193 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'W' and resid 143 through 146 removed outlier: 3.712A pdb=" N GLY W 156 " --> pdb=" O LEU W 171 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'X' and resid 367 through 371 removed outlier: 7.168A pdb=" N ALA X 74 " --> pdb=" O LEU X 368 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N VAL X 370 " --> pdb=" O ALA X 74 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N LEU X 76 " --> pdb=" O VAL X 370 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL X 336 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 7.717A pdb=" N LEU X 77 " --> pdb=" O VAL X 336 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU X 338 " --> pdb=" O LEU X 77 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU X 308 " --> pdb=" O VAL X 335 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'X' and resid 130 through 132 removed outlier: 3.689A pdb=" N ARG X 132 " --> pdb=" O GLU X 302 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU X 302 " --> pdb=" O ARG X 132 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'X' and resid 238 through 243 removed outlier: 3.799A pdb=" N LYS X 241 " --> pdb=" O LYS X 137 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS X 137 " --> pdb=" O LYS X 241 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU X 135 " --> pdb=" O ILE X 243 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY X 142 " --> pdb=" O ILE X 200 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N TYR X 201 " --> pdb=" O ARG X 211 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ARG X 211 " --> pdb=" O TYR X 201 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N GLU X 203 " --> pdb=" O VAL X 209 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL X 209 " --> pdb=" O GLU X 203 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'X' and resid 166 through 171 removed outlier: 4.520A pdb=" N VAL X 166 " --> pdb=" O LEU X 181 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU X 181 " --> pdb=" O VAL X 166 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'Y' and resid 351 through 356 removed outlier: 7.056A pdb=" N ALA Y 70 " --> pdb=" O ILE Y 352 " (cutoff:3.500A) removed outlier: 8.380A pdb=" N ILE Y 354 " --> pdb=" O ALA Y 70 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N LEU Y 72 " --> pdb=" O ILE Y 354 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N THR Y 356 " --> pdb=" O LEU Y 72 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA Y 74 " --> pdb=" O THR Y 356 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL Y 321 " --> pdb=" O VAL Y 71 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N VAL Y 73 " --> pdb=" O VAL Y 321 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N MET Y 323 " --> pdb=" O VAL Y 73 " (cutoff:3.500A) removed outlier: 8.389A pdb=" N GLY Y 75 " --> pdb=" O MET Y 323 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'Y' and resid 230 through 240 Processing sheet with id= AG, first strand: chain 'Y' and resid 135 through 138 removed outlier: 3.617A pdb=" N GLY Y 138 " --> pdb=" O ILE Y 190 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ILE Y 190 " --> pdb=" O GLY Y 138 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY Y 203 " --> pdb=" O VAL Y 189 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N SER Y 191 " --> pdb=" O LYS Y 201 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N LYS Y 201 " --> pdb=" O SER Y 191 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASP Y 193 " --> pdb=" O ILE Y 199 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE Y 199 " --> pdb=" O ASP Y 193 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'Y' and resid 143 through 146 removed outlier: 3.712A pdb=" N GLY Y 156 " --> pdb=" O LEU Y 171 " (cutoff:3.500A) 1361 hydrogen bonds defined for protein. 4005 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 421 hydrogen bonds 802 hydrogen bond angles 0 basepair planarities 167 basepair parallelities 294 stacking parallelities Total time for adding SS restraints: 25.58 Time building geometry restraints manager: 23.16 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: 11615 1.34 - 1.46: 9372 1.46 - 1.58: 23975 1.58 - 1.70: 716 1.70 - 1.82: 194 Bond restraints: 45872 Sorted by residual: bond pdb=" C VAL S 116 " pdb=" N PRO S 117 " ideal model delta sigma weight residual 1.337 1.401 -0.065 1.11e-02 8.12e+03 3.39e+01 bond pdb=" BE BEF R 502 " pdb=" F2 BEF R 502 " ideal model delta sigma weight residual 1.476 1.563 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" BE BEF M1602 " pdb=" F2 BEF M1602 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.80e+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 1.22e+01 ... (remaining 45867 not shown) Histogram of bond angle deviations from ideal: 97.05 - 104.94: 1935 104.94 - 112.82: 25807 112.82 - 120.71: 20701 120.71 - 128.59: 14678 128.59 - 136.47: 435 Bond angle restraints: 63556 Sorted by residual: angle pdb=" C PHE R 136 " pdb=" N VAL R 137 " pdb=" CA VAL R 137 " ideal model delta sigma weight residual 120.24 124.26 -4.02 6.30e-01 2.52e+00 4.07e+01 angle pdb=" C LEU M 998 " pdb=" N PHE M 999 " pdb=" CA PHE M 999 " ideal model delta sigma weight residual 126.32 135.68 -9.36 1.74e+00 3.30e-01 2.89e+01 angle pdb=" N LYS X 161 " pdb=" CA LYS X 161 " pdb=" C LYS X 161 " ideal model delta sigma weight residual 107.23 115.43 -8.20 1.67e+00 3.59e-01 2.41e+01 angle pdb=" C VAL M1068 " pdb=" N LYS M1069 " pdb=" CA LYS M1069 " ideal model delta sigma weight residual 123.93 131.43 -7.50 1.54e+00 4.22e-01 2.37e+01 angle pdb=" CA TYR X 462 " pdb=" CB TYR X 462 " pdb=" CG TYR X 462 " ideal model delta sigma weight residual 113.90 122.49 -8.59 1.80e+00 3.09e-01 2.28e+01 ... (remaining 63551 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.71: 24847 35.71 - 71.42: 2108 71.42 - 107.12: 51 107.12 - 142.83: 11 142.83 - 178.54: 4 Dihedral angle restraints: 27021 sinusoidal: 13070 harmonic: 13951 Sorted by residual: dihedral pdb=" CA GLY T 160 " pdb=" C GLY T 160 " pdb=" N LYS T 161 " pdb=" CA LYS T 161 " ideal model delta harmonic sigma weight residual -180.00 -126.60 -53.40 0 5.00e+00 4.00e-02 1.14e+02 dihedral pdb=" CA ASP X 151 " pdb=" C ASP X 151 " pdb=" N ALA X 152 " pdb=" CA ALA X 152 " ideal model delta harmonic sigma weight residual -180.00 -131.00 -49.00 0 5.00e+00 4.00e-02 9.61e+01 dihedral pdb=" CA PHE W 221 " pdb=" C PHE W 221 " pdb=" N VAL W 222 " pdb=" CA VAL W 222 " ideal model delta harmonic sigma weight residual 180.00 131.98 48.02 0 5.00e+00 4.00e-02 9.22e+01 ... (remaining 27018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 5700 0.045 - 0.090: 1269 0.090 - 0.135: 423 0.135 - 0.180: 37 0.180 - 0.225: 11 Chirality restraints: 7440 Sorted by residual: chirality pdb=" CA PHE M 999 " pdb=" N PHE M 999 " pdb=" C PHE M 999 " pdb=" CB PHE M 999 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" P DT J 25 " pdb=" OP1 DT J 25 " pdb=" OP2 DT J 25 " pdb=" O5' DT J 25 " both_signs ideal model delta sigma weight residual True 2.35 -2.56 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ARG M1133 " pdb=" N ARG M1133 " pdb=" C ARG M1133 " pdb=" CB ARG M1133 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 7437 not shown) Planarity restraints: 6874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER W 205 " 0.040 2.00e-02 2.50e+03 8.23e-02 6.77e+01 pdb=" C SER W 205 " -0.142 2.00e-02 2.50e+03 pdb=" O SER W 205 " 0.055 2.00e-02 2.50e+03 pdb=" N PHE W 206 " 0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER Y 205 " 0.035 2.00e-02 2.50e+03 6.97e-02 4.86e+01 pdb=" C SER Y 205 " -0.121 2.00e-02 2.50e+03 pdb=" O SER Y 205 " 0.046 2.00e-02 2.50e+03 pdb=" N PHE Y 206 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP X 151 " -0.020 2.00e-02 2.50e+03 4.03e-02 1.63e+01 pdb=" C ASP X 151 " 0.070 2.00e-02 2.50e+03 pdb=" O ASP X 151 " -0.026 2.00e-02 2.50e+03 pdb=" N ALA X 152 " -0.024 2.00e-02 2.50e+03 ... (remaining 6871 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 966 2.67 - 3.23: 36963 3.23 - 3.78: 72217 3.78 - 4.34: 94803 4.34 - 4.90: 146159 Nonbonded interactions: 351108 Sorted by model distance: nonbonded pdb=" O3B ADP M1601 " pdb=" BE BEF M1602 " model vdw 2.109 1.936 nonbonded pdb=" O1B ADP R 501 " pdb="MG MG R 503 " model vdw 2.170 2.170 nonbonded pdb=" O3B ADP X 501 " pdb="MG MG Y 501 " model vdw 2.178 2.170 nonbonded pdb=" F3 BEF M1602 " pdb="MG MG M1603 " model vdw 2.192 2.120 nonbonded pdb=" O3B ADP T 501 " pdb="MG MG U 501 " model vdw 2.237 2.170 ... (remaining 351103 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 or resid 502 throug \ h 503)) 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 or resid 501 through 502)) 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 or resid 502 through 503)) } 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: 8.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.290 Construct map_model_manager: 0.030 Extract box with map and model: 14.280 Check model and map are aligned: 0.590 Set scattering table: 0.360 Process input model: 145.960 Find NCS groups from input model: 2.650 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 175.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 45872 Z= 0.218 Angle : 0.755 14.190 63556 Z= 0.434 Chirality : 0.043 0.225 7440 Planarity : 0.005 0.082 6874 Dihedral : 20.637 178.540 17991 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.01 % Rotamer: Outliers : 8.77 % Allowed : 8.39 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.38 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.09), residues: 4633 helix: -3.92 (0.05), residues: 2130 sheet: -0.77 (0.20), residues: 580 loop : -2.36 (0.12), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 790 HIS 0.007 0.001 HIS U 153 PHE 0.014 0.001 PHE M1047 TYR 0.029 0.001 TYR V 462 ARG 0.004 0.000 ARG Y 208 *********************** 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 1505 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 1155 time to evaluate : 4.530 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: 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: 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.4546 (mt) cc_final: 0.4318 (mt) REVERT: B 131 ARG cc_start: 0.8259 (mtp180) cc_final: 0.7979 (mtp85) REVERT: C 70 VAL cc_start: 0.8574 (t) cc_final: 0.8324 (t) REVERT: C 78 ARG cc_start: 0.6949 (mtt180) cc_final: 0.6618 (ttm-80) REVERT: D 67 ARG cc_start: 0.8364 (tpt-90) cc_final: 0.8151 (ttp-110) REVERT: E 57 GLU cc_start: 0.7603 (tt0) cc_final: 0.6651 (tt0) REVERT: F 93 GLU cc_start: 0.8648 (mp0) cc_final: 0.8428 (mp0) REVERT: F 94 LEU cc_start: 0.8695 (mt) cc_final: 0.8450 (mt) REVERT: H 72 ILE cc_start: 0.8832 (mm) cc_final: 0.8344 (mm) REVERT: M 794 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7227 (p0) REVERT: M 937 VAL cc_start: 0.7061 (OUTLIER) cc_final: 0.6812 (t) REVERT: M 1039 ASP cc_start: 0.7924 (t70) cc_final: 0.7482 (t0) REVERT: M 1054 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7332 (tp) REVERT: M 1082 ASN cc_start: 0.6472 (OUTLIER) cc_final: 0.6088 (m-40) REVERT: M 1192 MET cc_start: 0.6490 (tpt) cc_final: 0.6277 (tpt) REVERT: M 1326 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7638 (tp) REVERT: R 226 LEU cc_start: 0.8111 (tp) cc_final: 0.7689 (tp) REVERT: R 230 THR cc_start: 0.7902 (p) cc_final: 0.7674 (t) REVERT: R 408 SER cc_start: 0.8927 (m) cc_final: 0.8687 (t) REVERT: S 12 THR cc_start: 0.8160 (m) cc_final: 0.7783 (m) REVERT: S 49 ILE cc_start: 0.7094 (mt) cc_final: 0.6619 (mm) REVERT: S 175 ILE cc_start: 0.8726 (mt) cc_final: 0.8508 (pt) REVERT: S 278 ARG cc_start: 0.5531 (mmt-90) cc_final: 0.5088 (tpm170) REVERT: T 133 ILE cc_start: -0.3733 (OUTLIER) cc_final: -0.4011 (mt) REVERT: T 182 ASP cc_start: 0.3031 (OUTLIER) cc_final: 0.2649 (t70) REVERT: T 202 ILE cc_start: 0.5247 (OUTLIER) cc_final: 0.4849 (tt) REVERT: T 226 THR cc_start: 0.5115 (OUTLIER) cc_final: 0.4731 (t) REVERT: T 233 PRO cc_start: 0.0224 (Cg_exo) cc_final: -0.0106 (Cg_endo) REVERT: T 456 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6732 (tp) REVERT: U 15 LYS cc_start: 0.6000 (OUTLIER) cc_final: 0.4993 (tptp) REVERT: U 136 ILE cc_start: 0.7432 (mt) cc_final: 0.7107 (tp) REVERT: U 252 GLN cc_start: 0.4484 (OUTLIER) cc_final: 0.3094 (tt0) REVERT: U 259 THR cc_start: 0.6839 (p) cc_final: 0.6277 (p) REVERT: V 24 THR cc_start: 0.7758 (m) cc_final: 0.7356 (p) REVERT: V 247 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7964 (p) REVERT: V 317 ASP cc_start: 0.8497 (t0) cc_final: 0.8261 (t70) REVERT: W 160 ILE cc_start: 0.8608 (mt) cc_final: 0.8272 (tp) REVERT: W 255 LEU cc_start: 0.8307 (mt) cc_final: 0.7946 (tp) REVERT: W 420 VAL cc_start: 0.6609 (OUTLIER) cc_final: 0.6051 (t) REVERT: X 153 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6959 (pm20) REVERT: X 162 THR cc_start: -0.0253 (OUTLIER) cc_final: -0.1005 (p) REVERT: X 163 ILE cc_start: 0.0102 (OUTLIER) cc_final: -0.0589 (mt) REVERT: Y 117 LEU cc_start: 0.7518 (tp) cc_final: 0.7225 (tp) REVERT: Y 135 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6982 (tt) REVERT: Y 160 ILE cc_start: 0.8727 (mt) cc_final: 0.8509 (tp) REVERT: Y 268 GLU cc_start: 0.2285 (OUTLIER) cc_final: -0.0625 (mm-30) REVERT: Y 456 ILE cc_start: 0.0232 (OUTLIER) cc_final: -0.0087 (pt) outliers start: 350 outliers final: 41 residues processed: 1423 average time/residue: 0.6606 time to fit residues: 1512.4787 Evaluate side-chains 560 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 499 time to evaluate : 4.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain M residue 794 ASP Chi-restraints excluded: chain M residue 937 VAL Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1038 VAL Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1054 LEU Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1068 VAL Chi-restraints excluded: chain M residue 1075 VAL Chi-restraints excluded: chain M residue 1082 ASN Chi-restraints excluded: chain M residue 1213 VAL Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1326 LEU Chi-restraints excluded: chain M residue 1386 LYS Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 331 VAL Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain T residue 159 TYR Chi-restraints excluded: chain T residue 182 ASP Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 226 THR Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 322 THR Chi-restraints excluded: chain T residue 456 LEU Chi-restraints excluded: chain U residue 15 LYS Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain U residue 273 ILE Chi-restraints excluded: chain V residue 247 VAL Chi-restraints excluded: chain V residue 278 THR Chi-restraints excluded: chain V residue 292 VAL Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 206 PHE Chi-restraints excluded: chain W residue 339 SER Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 153 GLU Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 219 THR Chi-restraints excluded: chain Y residue 221 PHE Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 320 ILE Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 429 optimal weight: 7.9990 chunk 385 optimal weight: 0.6980 chunk 214 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 260 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 398 optimal weight: 20.0000 chunk 154 optimal weight: 7.9990 chunk 242 optimal weight: 5.9990 chunk 296 optimal weight: 0.8980 chunk 462 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 HIS E 16 GLN E 42 GLN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 HIS F 39 ASN F 42 GLN H 112 HIS M 782 GLN M 857 GLN M1082 ASN M1173 ASN ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 45 HIS ** R 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 HIS ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 117 GLN R 247 ASN R 251 GLN R 359 ASN S 261 ASN T 124 ASN T 263 GLN ** T 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 289 ASN T 417 GLN T 461 ASN ** U 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN ** U 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 237 HIS ** U 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 455 GLN V 190 GLN ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 341 ASN V 357 HIS ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 63 ASN W 272 GLN W 401 ASN X 271 GLN X 289 ASN X 341 ASN X 357 HIS Y 23 HIS Y 63 ASN ** Y 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 230 GLN Y 326 ASN Y 408 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6311 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 45872 Z= 0.238 Angle : 0.724 10.504 63556 Z= 0.373 Chirality : 0.042 0.264 7440 Planarity : 0.005 0.059 6874 Dihedral : 23.871 155.414 9136 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.81 % Allowed : 18.66 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -2.26 (0.11), residues: 4633 helix: -1.39 (0.09), residues: 2119 sheet: -0.53 (0.20), residues: 646 loop : -1.84 (0.12), residues: 1868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP M 790 HIS 0.022 0.001 HIS U 153 PHE 0.031 0.002 PHE M 764 TYR 0.027 0.002 TYR V 323 ARG 0.018 0.001 ARG X 381 *********************** 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 713 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 521 time to evaluate : 4.443 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 LYS cc_start: 0.8671 (tppt) cc_final: 0.7990 (mmmt) REVERT: E 57 GLU cc_start: 0.7840 (tt0) cc_final: 0.7449 (tt0) REVERT: F 93 GLU cc_start: 0.8840 (mp0) cc_final: 0.8634 (mp0) REVERT: G 46 LYS cc_start: 0.8865 (mmmt) cc_final: 0.8664 (tptt) REVERT: G 108 GLU cc_start: 0.8228 (mp0) cc_final: 0.7810 (tp30) REVERT: H 102 ARG cc_start: 0.7917 (mmm160) cc_final: 0.7386 (mmp80) REVERT: H 104 ILE cc_start: 0.9018 (tp) cc_final: 0.8790 (tp) REVERT: H 105 LEU cc_start: 0.8127 (mm) cc_final: 0.7837 (tp) REVERT: M 821 MET cc_start: 0.5668 (ptt) cc_final: 0.5316 (ptp) REVERT: M 999 PHE cc_start: 0.6292 (OUTLIER) cc_final: 0.4538 (m-80) REVERT: M 1326 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7387 (tp) REVERT: R 238 MET cc_start: 0.7278 (tpp) cc_final: 0.6860 (tpt) REVERT: S 278 ARG cc_start: 0.6106 (mmt-90) cc_final: 0.5477 (tpm170) REVERT: T 70 MET cc_start: 0.2173 (mmt) cc_final: 0.1918 (tpp) REVERT: T 133 ILE cc_start: -0.3250 (OUTLIER) cc_final: -0.3622 (mt) REVERT: T 159 TYR cc_start: 0.6576 (OUTLIER) cc_final: 0.6319 (m-80) REVERT: T 182 ASP cc_start: 0.3282 (OUTLIER) cc_final: 0.2598 (t70) REVERT: U 15 LYS cc_start: 0.6378 (OUTLIER) cc_final: 0.6073 (tptp) REVERT: U 175 MET cc_start: 0.5023 (mtm) cc_final: 0.4250 (mtm) REVERT: U 252 GLN cc_start: 0.4917 (OUTLIER) cc_final: 0.4216 (pt0) REVERT: V 24 THR cc_start: 0.8037 (m) cc_final: 0.7643 (p) REVERT: V 111 TYR cc_start: 0.6712 (m-80) cc_final: 0.5734 (m-80) REVERT: V 221 GLU cc_start: 0.7652 (mm-30) cc_final: 0.6853 (mm-30) REVERT: V 309 PHE cc_start: 0.7513 (t80) cc_final: 0.7129 (t80) REVERT: V 367 LEU cc_start: 0.8422 (mt) cc_final: 0.8159 (mt) REVERT: W 169 TYR cc_start: 0.7896 (m-10) cc_final: 0.7645 (m-10) REVERT: W 255 LEU cc_start: 0.8463 (mt) cc_final: 0.8074 (tp) REVERT: Y 135 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7107 (tt) REVERT: Y 160 ILE cc_start: 0.8934 (mt) cc_final: 0.8693 (tp) REVERT: Y 456 ILE cc_start: -0.0621 (OUTLIER) cc_final: -0.1618 (mm) outliers start: 192 outliers final: 105 residues processed: 673 average time/residue: 0.5617 time to fit residues: 624.8089 Evaluate side-chains 500 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 386 time to evaluate : 5.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 86 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 125 SER Chi-restraints excluded: chain M residue 686 VAL Chi-restraints excluded: chain M residue 695 ASN Chi-restraints excluded: chain M residue 696 LEU Chi-restraints excluded: chain M residue 734 LEU Chi-restraints excluded: chain M residue 823 LEU Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1068 VAL Chi-restraints excluded: chain M residue 1075 VAL Chi-restraints excluded: chain M residue 1085 LEU Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1152 TYR Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1316 VAL Chi-restraints excluded: chain M residue 1326 LEU Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1386 LYS Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 47 LYS Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 308 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 193 ASN Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 60 VAL Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain T residue 159 TYR Chi-restraints excluded: chain T residue 182 ASP Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain U residue 15 LYS Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 236 VAL Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain U residue 325 THR Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 416 ASN Chi-restraints excluded: chain U residue 420 VAL Chi-restraints excluded: chain V residue 105 LEU Chi-restraints excluded: chain V residue 144 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 245 GLN Chi-restraints excluded: chain V residue 264 ASP Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 158 LEU Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 191 SER Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 305 CYS Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 339 SER Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 243 ILE Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 313 VAL Chi-restraints excluded: chain X residue 331 ASN Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 369 ILE Chi-restraints excluded: chain X residue 435 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 158 LEU Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 219 THR Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 273 ILE Chi-restraints excluded: chain Y residue 303 ILE Chi-restraints excluded: chain Y residue 320 ILE Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 354 ILE Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 256 optimal weight: 6.9990 chunk 143 optimal weight: 9.9990 chunk 384 optimal weight: 4.9990 chunk 314 optimal weight: 0.3980 chunk 127 optimal weight: 7.9990 chunk 463 optimal weight: 1.9990 chunk 500 optimal weight: 3.9990 chunk 412 optimal weight: 0.5980 chunk 459 optimal weight: 9.9990 chunk 157 optimal weight: 30.0000 chunk 371 optimal weight: 9.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN E 39 ASN H 70 ASN ** M 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 712 ASN M 730 GLN M 873 GLN ** M1044 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M1070 ASN M1226 GLN M1285 HIS ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 61 HIS ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 422 HIS S 261 ASN ** T 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 360 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 94 GLN V 124 ASN V 245 GLN V 256 ASN V 271 GLN V 394 GLN ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 299 HIS W 416 ASN X 205 ASN ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 341 ASN Y 326 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6575 moved from start: 0.5189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 45872 Z= 0.262 Angle : 0.707 9.923 63556 Z= 0.365 Chirality : 0.042 0.196 7440 Planarity : 0.005 0.071 6874 Dihedral : 23.748 149.316 9099 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.01 % Allowed : 18.44 % Favored : 75.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -1.31 (0.11), residues: 4633 helix: -0.29 (0.10), residues: 2116 sheet: -0.39 (0.21), residues: 624 loop : -1.62 (0.13), residues: 1893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP U 280 HIS 0.016 0.002 HIS U 153 PHE 0.029 0.002 PHE M 796 TYR 0.038 0.002 TYR T 323 ARG 0.016 0.001 ARG E 36 *********************** 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 668 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 428 time to evaluate : 4.543 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: 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 ARG cc_start: 0.7112 (mmt180) cc_final: 0.6728 (mmt180) REVERT: E 57 GLU cc_start: 0.7956 (tt0) cc_final: 0.7576 (tt0) REVERT: F 93 GLU cc_start: 0.8819 (mp0) cc_final: 0.8500 (mp0) REVERT: G 46 LYS cc_start: 0.8892 (mmmt) cc_final: 0.8592 (tptt) REVERT: G 105 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7810 (mm) REVERT: H 102 ARG cc_start: 0.7822 (mmm160) cc_final: 0.7173 (mmp80) REVERT: M 723 MET cc_start: 0.8151 (pmm) cc_final: 0.7643 (ppp) REVERT: M 821 MET cc_start: 0.5546 (ptt) cc_final: 0.5296 (ptp) REVERT: M 1037 ARG cc_start: 0.8271 (mmp80) cc_final: 0.8050 (ttp-170) REVERT: M 1131 ASP cc_start: 0.8712 (t0) cc_final: 0.8370 (t70) REVERT: M 1326 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7598 (tp) REVERT: R 226 LEU cc_start: 0.8621 (tp) cc_final: 0.8227 (tp) REVERT: R 238 MET cc_start: 0.7255 (tpp) cc_final: 0.6903 (tpp) REVERT: R 349 MET cc_start: 0.8278 (mmm) cc_final: 0.7558 (mmt) REVERT: S 278 ARG cc_start: 0.6230 (mmt-90) cc_final: 0.5442 (tpm170) REVERT: T 194 VAL cc_start: -0.1240 (OUTLIER) cc_final: -0.1480 (t) REVERT: U 252 GLN cc_start: 0.5175 (OUTLIER) cc_final: 0.4534 (mt0) REVERT: V 367 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8093 (mt) REVERT: V 406 MET cc_start: 0.9075 (tpp) cc_final: 0.8696 (mmm) REVERT: W 206 PHE cc_start: 0.6931 (OUTLIER) cc_final: 0.6454 (p90) REVERT: W 255 LEU cc_start: 0.8240 (mt) cc_final: 0.7841 (tp) REVERT: X 150 GLU cc_start: 0.2771 (OUTLIER) cc_final: 0.2155 (pm20) REVERT: X 284 LEU cc_start: 0.7208 (tp) cc_final: 0.6969 (tp) REVERT: Y 117 LEU cc_start: 0.8290 (tp) cc_final: 0.8068 (tp) REVERT: Y 135 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7493 (tt) REVERT: Y 160 ILE cc_start: 0.9087 (mt) cc_final: 0.8767 (tp) REVERT: Y 198 LYS cc_start: 0.4527 (OUTLIER) cc_final: 0.4059 (mtmm) REVERT: Y 268 GLU cc_start: 0.3867 (OUTLIER) cc_final: 0.0535 (mm-30) REVERT: Y 456 ILE cc_start: -0.0787 (OUTLIER) cc_final: -0.1346 (tp) outliers start: 240 outliers final: 122 residues processed: 620 average time/residue: 0.5323 time to fit residues: 547.7994 Evaluate side-chains 485 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 352 time to evaluate : 4.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 32 HIS Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 104 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain M residue 686 VAL Chi-restraints excluded: chain M residue 695 ASN Chi-restraints excluded: chain M residue 696 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 701 LYS Chi-restraints excluded: chain M residue 718 ILE Chi-restraints excluded: chain M residue 734 LEU Chi-restraints excluded: chain M residue 773 VAL Chi-restraints excluded: chain M residue 871 MET Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1013 CYS Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1048 THR Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1070 ASN Chi-restraints excluded: chain M residue 1075 VAL Chi-restraints excluded: chain M residue 1085 LEU Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1232 THR Chi-restraints excluded: chain M residue 1316 VAL Chi-restraints excluded: chain M residue 1326 LEU Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1386 LYS Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 308 ASP Chi-restraints excluded: chain R residue 355 CYS Chi-restraints excluded: chain R residue 369 LEU Chi-restraints excluded: chain S residue 12 THR Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 193 ASN Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 159 TYR Chi-restraints excluded: chain T residue 194 VAL Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 453 THR Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 137 GLU Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 236 VAL Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain U residue 255 LEU Chi-restraints excluded: chain U residue 258 PHE Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 416 ASN Chi-restraints excluded: chain U residue 429 LEU Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 108 SER Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 226 THR Chi-restraints excluded: chain V residue 264 ASP Chi-restraints excluded: chain V residue 278 THR Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 362 ASP Chi-restraints excluded: chain V residue 367 LEU Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 145 ILE Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 206 PHE Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 339 SER Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 448 ILE Chi-restraints excluded: chain W residue 454 VAL Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 150 GLU Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 331 ASN Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 359 VAL Chi-restraints excluded: chain X residue 392 ARG Chi-restraints excluded: chain X residue 435 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 198 LYS Chi-restraints excluded: chain Y residue 199 ILE Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 303 ILE Chi-restraints excluded: chain Y residue 320 ILE Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 354 ILE Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 457 optimal weight: 7.9990 chunk 348 optimal weight: 0.0670 chunk 240 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 220 optimal weight: 0.5980 chunk 310 optimal weight: 8.9990 chunk 464 optimal weight: 7.9990 chunk 492 optimal weight: 0.9990 chunk 242 optimal weight: 5.9990 chunk 440 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 113 HIS M 702 GLN M 712 ASN M 873 GLN M1044 ASN ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 106 ASN T 205 ASN ** T 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 360 ASN ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 341 ASN Y 252 GLN ** Y 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6569 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 45872 Z= 0.181 Angle : 0.631 10.744 63556 Z= 0.322 Chirality : 0.040 0.293 7440 Planarity : 0.004 0.053 6874 Dihedral : 23.551 149.965 9083 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.68 % Allowed : 19.96 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.83 (0.12), residues: 4633 helix: 0.30 (0.11), residues: 2111 sheet: -0.44 (0.21), residues: 617 loop : -1.51 (0.13), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 790 HIS 0.012 0.001 HIS U 153 PHE 0.023 0.001 PHE R 360 TYR 0.034 0.001 TYR G 86 ARG 0.006 0.000 ARG T 366 *********************** 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 578 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 391 time to evaluate : 4.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 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: symmetry clash REVERT: A 100 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7994 (mm) REVERT: A 108 ASN cc_start: 0.7700 (OUTLIER) cc_final: 0.7464 (t0) REVERT: B 83 ARG cc_start: 0.7279 (mmt180) cc_final: 0.6945 (mtt-85) REVERT: E 57 GLU cc_start: 0.7873 (tt0) cc_final: 0.7520 (tt0) REVERT: F 93 GLU cc_start: 0.8829 (mp0) cc_final: 0.8524 (mp0) REVERT: G 46 LYS cc_start: 0.8855 (mmmt) cc_final: 0.8588 (tptt) REVERT: G 75 ARG cc_start: 0.8698 (mmm160) cc_final: 0.8404 (tpp80) REVERT: H 96 GLU cc_start: 0.7737 (mp0) cc_final: 0.6905 (mp0) REVERT: H 102 ARG cc_start: 0.7865 (mmm160) cc_final: 0.7294 (mmp80) REVERT: M 723 MET cc_start: 0.7784 (pmm) cc_final: 0.7278 (ppp) REVERT: M 764 PHE cc_start: 0.8093 (m-80) cc_final: 0.7890 (m-80) REVERT: M 1032 ASN cc_start: 0.6430 (OUTLIER) cc_final: 0.6202 (p0) REVERT: M 1214 MET cc_start: 0.8546 (mtt) cc_final: 0.8309 (mtt) REVERT: M 1326 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7431 (tp) REVERT: R 226 LEU cc_start: 0.8488 (tp) cc_final: 0.8197 (tp) REVERT: R 238 MET cc_start: 0.7519 (tpp) cc_final: 0.7189 (tpt) REVERT: S 278 ARG cc_start: 0.6308 (mmt-90) cc_final: 0.5374 (tpm170) REVERT: T 70 MET cc_start: 0.3063 (ttm) cc_final: 0.1825 (ptp) REVERT: T 75 ILE cc_start: 0.7285 (mm) cc_final: 0.7069 (mt) REVERT: U 142 GLU cc_start: 0.4380 (mm-30) cc_final: 0.4122 (mm-30) REVERT: U 252 GLN cc_start: 0.4807 (OUTLIER) cc_final: 0.4524 (pt0) REVERT: U 323 MET cc_start: 0.8102 (mpp) cc_final: 0.7792 (mpp) REVERT: V 309 PHE cc_start: 0.7521 (t80) cc_final: 0.7282 (t80) REVERT: V 367 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8436 (mt) REVERT: V 406 MET cc_start: 0.9026 (tpp) cc_final: 0.8697 (mmm) REVERT: W 255 LEU cc_start: 0.8358 (mt) cc_final: 0.7942 (tp) REVERT: X 236 GLU cc_start: 0.6295 (pm20) cc_final: 0.6017 (pm20) REVERT: X 329 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: Y 135 LEU cc_start: 0.7748 (OUTLIER) cc_final: 0.7539 (tt) REVERT: Y 160 ILE cc_start: 0.8998 (mt) cc_final: 0.8748 (tp) REVERT: Y 165 MET cc_start: 0.6617 (tpt) cc_final: 0.6391 (mpp) REVERT: Y 198 LYS cc_start: 0.4639 (OUTLIER) cc_final: 0.4328 (mtmm) REVERT: Y 268 GLU cc_start: 0.3727 (OUTLIER) cc_final: 0.0455 (mm-30) REVERT: Y 456 ILE cc_start: -0.0409 (OUTLIER) cc_final: -0.0924 (tp) outliers start: 187 outliers final: 119 residues processed: 539 average time/residue: 0.5373 time to fit residues: 484.0699 Evaluate side-chains 474 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 344 time to evaluate : 4.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 32 HIS Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain M residue 686 VAL Chi-restraints excluded: chain M residue 695 ASN Chi-restraints excluded: chain M residue 696 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 701 LYS Chi-restraints excluded: chain M residue 702 GLN Chi-restraints excluded: chain M residue 718 ILE Chi-restraints excluded: chain M residue 734 LEU Chi-restraints excluded: chain M residue 773 VAL Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1005 LEU Chi-restraints excluded: chain M residue 1013 CYS Chi-restraints excluded: chain M residue 1032 ASN Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1075 VAL Chi-restraints excluded: chain M residue 1085 LEU Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1316 VAL Chi-restraints excluded: chain M residue 1326 LEU Chi-restraints excluded: chain M residue 1340 ASP Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1386 LYS Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 308 ASP Chi-restraints excluded: chain R residue 369 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 192 THR Chi-restraints excluded: chain S residue 193 ASN Chi-restraints excluded: chain T residue 159 TYR Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 285 ARG Chi-restraints excluded: chain T residue 311 ASP Chi-restraints excluded: chain T residue 313 VAL Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 363 LEU Chi-restraints excluded: chain U residue 24 SER Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 95 ASP Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 136 ILE Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 173 ASN Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 236 VAL Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain U residue 258 PHE Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 416 ASN Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 264 ASP Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 367 LEU Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 339 SER Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain W residue 367 ILE Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 448 ILE Chi-restraints excluded: chain X residue 36 ASP Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 133 ILE Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 329 GLU Chi-restraints excluded: chain X residue 331 ASN Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 341 ASN Chi-restraints excluded: chain X residue 359 VAL Chi-restraints excluded: chain X residue 369 ILE Chi-restraints excluded: chain X residue 392 ARG Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 92 LEU Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 198 LYS Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 215 MET Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 354 ILE Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 407 GLN Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 409 optimal weight: 0.6980 chunk 279 optimal weight: 7.9990 chunk 7 optimal weight: 30.0000 chunk 366 optimal weight: 9.9990 chunk 203 optimal weight: 9.9990 chunk 419 optimal weight: 5.9990 chunk 340 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 251 optimal weight: 9.9990 chunk 441 optimal weight: 7.9990 chunk 124 optimal weight: 7.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN M 712 ASN M 873 GLN M1070 ASN M1249 GLN M1263 HIS ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 HIS R 98 HIS ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 HIS R 374 GLN ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 273 ASN ** T 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 238 HIS ** T 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 394 GLN ** T 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 29 HIS ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 455 GLN ** X 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 314 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 237 HIS ** Y 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 252 GLN Y 455 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.8120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.230 45872 Z= 0.530 Angle : 1.028 17.370 63556 Z= 0.536 Chirality : 0.053 0.341 7440 Planarity : 0.008 0.102 6874 Dihedral : 24.092 148.183 9079 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 33.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.93 % Favored : 93.03 % Rotamer: Outliers : 7.49 % Allowed : 19.76 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.11), residues: 4633 helix: -0.70 (0.10), residues: 2090 sheet: -0.89 (0.20), residues: 617 loop : -2.00 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP Y 280 HIS 0.032 0.003 HIS Y 299 PHE 0.042 0.004 PHE Y 221 TYR 0.044 0.004 TYR G 86 ARG 0.027 0.002 ARG Y 204 *********************** 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 658 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 359 time to evaluate : 4.576 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: 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 131 ARG cc_start: 0.8446 (OUTLIER) cc_final: 0.7693 (ttp-170) REVERT: B 83 ARG cc_start: 0.7347 (mmt180) cc_final: 0.7060 (mtt180) REVERT: C 58 LEU cc_start: 0.9588 (OUTLIER) cc_final: 0.9180 (tm) REVERT: E 57 GLU cc_start: 0.7905 (tt0) cc_final: 0.7616 (tt0) REVERT: G 36 ARG cc_start: 0.5426 (ttt180) cc_final: 0.4785 (mmp80) REVERT: G 46 LYS cc_start: 0.8939 (mmmt) cc_final: 0.8631 (tptt) REVERT: H 108 GLU cc_start: 0.7177 (tp30) cc_final: 0.6936 (tp30) REVERT: M 737 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.8384 (t80) REVERT: M 830 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8912 (pttm) REVERT: M 1053 ASP cc_start: 0.8952 (p0) cc_final: 0.8727 (p0) REVERT: R 69 TRP cc_start: 0.6732 (OUTLIER) cc_final: 0.4821 (m100) REVERT: R 238 MET cc_start: 0.7814 (tpp) cc_final: 0.7365 (mmm) REVERT: R 324 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8697 (mp10) REVERT: R 330 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.6764 (mm) REVERT: S 278 ARG cc_start: 0.6894 (mmt-90) cc_final: 0.5474 (tpm170) REVERT: T 303 LEU cc_start: 0.4420 (OUTLIER) cc_final: 0.4188 (tm) REVERT: U 188 ASP cc_start: 0.7061 (OUTLIER) cc_final: 0.6772 (t0) REVERT: W 29 LEU cc_start: 0.7946 (tp) cc_final: 0.7686 (tp) REVERT: W 128 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8607 (ttpp) REVERT: W 169 TYR cc_start: 0.7616 (m-10) cc_final: 0.7306 (m-10) REVERT: W 255 LEU cc_start: 0.8808 (mt) cc_final: 0.7987 (tp) REVERT: X 53 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7292 (tm-30) REVERT: X 315 MET cc_start: 0.3343 (ptm) cc_final: 0.1464 (mmm) REVERT: X 331 ASN cc_start: 0.7308 (OUTLIER) cc_final: 0.7068 (p0) REVERT: Y 44 MET cc_start: 0.3257 (mtp) cc_final: 0.3000 (mtp) REVERT: Y 117 LEU cc_start: 0.8438 (tp) cc_final: 0.7975 (tt) REVERT: Y 135 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7921 (tt) REVERT: Y 160 ILE cc_start: 0.9185 (mt) cc_final: 0.8947 (tp) REVERT: Y 268 GLU cc_start: 0.5648 (OUTLIER) cc_final: 0.5309 (pt0) REVERT: Y 456 ILE cc_start: -0.2346 (OUTLIER) cc_final: -0.3131 (tp) outliers start: 299 outliers final: 172 residues processed: 609 average time/residue: 0.5863 time to fit residues: 594.1272 Evaluate side-chains 484 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 298 time to evaluate : 4.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 53 GLU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain D residue 100 PHE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain F residue 100 ASN Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 70 ASN Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain G residue 124 TYR Chi-restraints excluded: chain H residue 54 ASP Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain M residue 695 ASN Chi-restraints excluded: chain M residue 696 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 701 LYS Chi-restraints excluded: chain M residue 718 ILE Chi-restraints excluded: chain M residue 734 LEU Chi-restraints excluded: chain M residue 737 TYR Chi-restraints excluded: chain M residue 830 LYS Chi-restraints excluded: chain M residue 858 ASN Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1048 THR Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1070 ASN Chi-restraints excluded: chain M residue 1075 VAL Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1150 VAL Chi-restraints excluded: chain M residue 1152 TYR Chi-restraints excluded: chain M residue 1183 LEU Chi-restraints excluded: chain M residue 1199 LEU Chi-restraints excluded: chain M residue 1232 THR Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1316 VAL Chi-restraints excluded: chain M residue 1339 TYR Chi-restraints excluded: chain M residue 1340 ASP Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 47 LYS Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 69 TRP Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 286 TYR Chi-restraints excluded: chain R residue 308 ASP Chi-restraints excluded: chain R residue 324 GLN Chi-restraints excluded: chain R residue 330 ILE Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 8 ILE Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain S residue 193 ASN Chi-restraints excluded: chain S residue 244 CYS Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 227 GLU Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 237 VAL Chi-restraints excluded: chain T residue 285 ARG Chi-restraints excluded: chain T residue 303 LEU Chi-restraints excluded: chain T residue 311 ASP Chi-restraints excluded: chain T residue 322 THR Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 353 VAL Chi-restraints excluded: chain T residue 357 HIS Chi-restraints excluded: chain T residue 453 THR Chi-restraints excluded: chain T residue 455 ILE Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 95 ASP Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 121 PHE Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 188 ASP Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 229 LEU Chi-restraints excluded: chain U residue 236 VAL Chi-restraints excluded: chain U residue 251 THR Chi-restraints excluded: chain U residue 259 THR Chi-restraints excluded: chain U residue 315 ASP Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 416 ASN Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 103 CYS Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 205 ASN Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 264 ASP Chi-restraints excluded: chain V residue 362 ASP Chi-restraints excluded: chain W residue 35 LEU Chi-restraints excluded: chain W residue 82 THR Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 128 LYS Chi-restraints excluded: chain W residue 145 ILE Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 265 ILE Chi-restraints excluded: chain W residue 282 GLU Chi-restraints excluded: chain W residue 302 ASP Chi-restraints excluded: chain W residue 323 MET Chi-restraints excluded: chain W residue 325 THR Chi-restraints excluded: chain W residue 339 SER Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 422 ASP Chi-restraints excluded: chain W residue 448 ILE Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 324 LEU Chi-restraints excluded: chain X residue 331 ASN Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 369 ILE Chi-restraints excluded: chain X residue 392 ARG Chi-restraints excluded: chain X residue 435 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 20 ILE Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 184 VAL Chi-restraints excluded: chain Y residue 191 SER Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 219 THR Chi-restraints excluded: chain Y residue 242 HIS Chi-restraints excluded: chain Y residue 262 THR Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 303 ILE Chi-restraints excluded: chain Y residue 321 VAL Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 359 TYR Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Y residue 420 VAL Chi-restraints excluded: chain Y residue 454 VAL Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 165 optimal weight: 3.9990 chunk 443 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 288 optimal weight: 7.9990 chunk 121 optimal weight: 2.9990 chunk 492 optimal weight: 4.9990 chunk 408 optimal weight: 9.9990 chunk 228 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 162 optimal weight: 4.9990 chunk 258 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 873 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M1032 ASN ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 63 ASN ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 165 HIS ** Y 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.8493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 45872 Z= 0.323 Angle : 0.771 13.126 63556 Z= 0.401 Chirality : 0.045 0.209 7440 Planarity : 0.005 0.071 6874 Dihedral : 23.905 147.866 9061 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 24.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 5.04 % Allowed : 23.10 % Favored : 71.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.55 (0.12), residues: 4633 helix: -0.18 (0.11), residues: 2086 sheet: -0.89 (0.20), residues: 608 loop : -1.98 (0.13), residues: 1939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP Y 280 HIS 0.013 0.002 HIS G 112 PHE 0.035 0.002 PHE M 764 TYR 0.064 0.002 TYR G 86 ARG 0.015 0.001 ARG Y 204 *********************** 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 545 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 344 time to evaluate : 4.820 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: 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: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7672 (ttp-170) REVERT: B 83 ARG cc_start: 0.7484 (mmt180) cc_final: 0.7034 (mtt180) REVERT: C 58 LEU cc_start: 0.9566 (OUTLIER) cc_final: 0.9139 (tm) REVERT: C 100 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.7184 (m-80) REVERT: E 57 GLU cc_start: 0.7920 (tt0) cc_final: 0.7642 (tt0) REVERT: G 46 LYS cc_start: 0.8917 (mmmt) cc_final: 0.8673 (tptt) REVERT: H 65 LEU cc_start: 0.9505 (tp) cc_final: 0.9041 (pp) REVERT: H 76 ILE cc_start: 0.8562 (OUTLIER) cc_final: 0.8301 (mm) REVERT: H 108 GLU cc_start: 0.7064 (tp30) cc_final: 0.6688 (tm-30) REVERT: M 737 TYR cc_start: 0.8827 (OUTLIER) cc_final: 0.8465 (t80) REVERT: M 1214 MET cc_start: 0.8420 (mtt) cc_final: 0.8218 (mtt) REVERT: R 238 MET cc_start: 0.8113 (tpp) cc_final: 0.7624 (tpp) REVERT: R 349 MET cc_start: 0.8766 (mmm) cc_final: 0.8529 (mmm) REVERT: R 369 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.9018 (mm) REVERT: S 20 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.8512 (p) REVERT: S 103 MET cc_start: 0.8002 (tpt) cc_final: 0.7759 (ttt) REVERT: S 278 ARG cc_start: 0.6981 (mmt-90) cc_final: 0.5465 (tpm170) REVERT: T 216 ASP cc_start: 0.7467 (t0) cc_final: 0.6926 (p0) REVERT: T 232 LEU cc_start: 0.6637 (tp) cc_final: 0.6356 (tt) REVERT: T 338 LEU cc_start: 0.6924 (mt) cc_final: 0.6701 (mp) REVERT: U 295 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8505 (pt) REVERT: U 416 ASN cc_start: 0.8700 (OUTLIER) cc_final: 0.7970 (t0) REVERT: V 264 ASP cc_start: 0.8175 (OUTLIER) cc_final: 0.7956 (m-30) REVERT: W 29 LEU cc_start: 0.7862 (tp) cc_final: 0.7638 (tp) REVERT: W 169 TYR cc_start: 0.7529 (m-10) cc_final: 0.7310 (m-10) REVERT: W 255 LEU cc_start: 0.8866 (mt) cc_final: 0.8109 (tp) REVERT: X 53 GLU cc_start: 0.7838 (mm-30) cc_final: 0.7280 (pm20) REVERT: X 122 MET cc_start: 0.5142 (ptp) cc_final: 0.4399 (ptp) REVERT: X 315 MET cc_start: 0.3436 (ptm) cc_final: 0.2135 (mmm) REVERT: X 323 TYR cc_start: 0.6063 (m-80) cc_final: 0.5730 (m-80) REVERT: X 344 MET cc_start: 0.1579 (mmp) cc_final: -0.0328 (tpp) REVERT: X 387 ARG cc_start: 0.6937 (tpt170) cc_final: 0.6401 (tpt170) REVERT: Y 117 LEU cc_start: 0.8531 (tp) cc_final: 0.8116 (tt) REVERT: Y 135 LEU cc_start: 0.8345 (mt) cc_final: 0.8110 (tt) REVERT: Y 268 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5527 (pt0) REVERT: Y 456 ILE cc_start: -0.1927 (OUTLIER) cc_final: -0.2787 (tp) outliers start: 201 outliers final: 138 residues processed: 511 average time/residue: 0.5361 time to fit residues: 457.9307 Evaluate side-chains 451 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 301 time to evaluate : 4.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 87 SER Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 104 PHE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 70 VAL Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain C residue 100 PHE Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 92 ASP Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 124 TYR Chi-restraints excluded: chain H residue 76 ILE Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain M residue 695 ASN Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 701 LYS Chi-restraints excluded: chain M residue 718 ILE Chi-restraints excluded: chain M residue 734 LEU Chi-restraints excluded: chain M residue 737 TYR Chi-restraints excluded: chain M residue 858 ASN Chi-restraints excluded: chain M residue 871 MET Chi-restraints excluded: chain M residue 1025 LEU Chi-restraints excluded: chain M residue 1032 ASN Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1075 VAL Chi-restraints excluded: chain M residue 1085 LEU Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1150 VAL Chi-restraints excluded: chain M residue 1152 TYR Chi-restraints excluded: chain M residue 1232 THR Chi-restraints excluded: chain M residue 1271 MET Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1316 VAL Chi-restraints excluded: chain M residue 1340 ASP Chi-restraints excluded: chain M residue 1351 CYS Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 47 LYS Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 87 ASP Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 287 VAL Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 308 ASP Chi-restraints excluded: chain R residue 369 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 20 THR Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain S residue 193 ASN Chi-restraints excluded: chain S residue 244 CYS Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 188 SER Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 212 VAL Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 285 ARG Chi-restraints excluded: chain T residue 311 ASP Chi-restraints excluded: chain T residue 332 ILE Chi-restraints excluded: chain T residue 453 THR Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 62 GLN Chi-restraints excluded: chain U residue 95 ASP Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 179 LEU Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 236 VAL Chi-restraints excluded: chain U residue 259 THR Chi-restraints excluded: chain U residue 295 ILE Chi-restraints excluded: chain U residue 315 ASP Chi-restraints excluded: chain U residue 339 SER Chi-restraints excluded: chain U residue 416 ASN Chi-restraints excluded: chain V residue 24 THR Chi-restraints excluded: chain V residue 62 VAL Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 92 ILE Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 199 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 264 ASP Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 362 ASP Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 145 ILE Chi-restraints excluded: chain W residue 150 THR Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 265 ILE Chi-restraints excluded: chain W residue 282 GLU Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain W residue 367 ILE Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain W residue 422 ASP Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 76 LEU Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 324 LEU Chi-restraints excluded: chain X residue 359 VAL Chi-restraints excluded: chain X residue 369 ILE Chi-restraints excluded: chain X residue 392 ARG Chi-restraints excluded: chain X residue 395 VAL Chi-restraints excluded: chain X residue 435 VAL Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 118 THR Chi-restraints excluded: chain Y residue 139 GLU Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 211 ASP Chi-restraints excluded: chain Y residue 262 THR Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 303 ILE Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 359 TYR Chi-restraints excluded: chain Y residue 365 LYS Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 411 MET Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 474 optimal weight: 0.1980 chunk 55 optimal weight: 0.0870 chunk 280 optimal weight: 9.9990 chunk 359 optimal weight: 5.9990 chunk 278 optimal weight: 7.9990 chunk 414 optimal weight: 8.9990 chunk 275 optimal weight: 0.8980 chunk 490 optimal weight: 0.8980 chunk 307 optimal weight: 7.9990 chunk 299 optimal weight: 1.9990 chunk 226 optimal weight: 5.9990 overall best weight: 0.8160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN M 873 GLN ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 359 ASN ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 273 ASN ** T 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 47 GLN ** U 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 34 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.8376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 45872 Z= 0.182 Angle : 0.678 11.366 63556 Z= 0.345 Chirality : 0.042 0.207 7440 Planarity : 0.004 0.056 6874 Dihedral : 23.524 148.796 9051 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.48 % Allowed : 24.87 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.12), residues: 4633 helix: 0.44 (0.11), residues: 2109 sheet: -0.73 (0.21), residues: 591 loop : -1.63 (0.13), residues: 1933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP U 280 HIS 0.009 0.001 HIS U 153 PHE 0.031 0.001 PHE T 309 TYR 0.042 0.002 TYR C 88 ARG 0.009 0.001 ARG X 73 *********************** 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 500 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 361 time to evaluate : 5.071 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 ARG cc_start: 0.7470 (mmt180) cc_final: 0.7135 (mtt180) REVERT: E 57 GLU cc_start: 0.7810 (tt0) cc_final: 0.7528 (tt0) REVERT: F 114 GLN cc_start: 0.8111 (tm-30) cc_final: 0.7759 (tm-30) REVERT: H 105 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7841 (tp) REVERT: H 108 GLU cc_start: 0.6899 (tp30) cc_final: 0.6675 (tm-30) REVERT: M 777 TYR cc_start: 0.5050 (OUTLIER) cc_final: 0.4688 (m-80) REVERT: M 1143 LEU cc_start: 0.8583 (mt) cc_final: 0.8158 (pp) REVERT: M 1214 MET cc_start: 0.8365 (mtt) cc_final: 0.8106 (mtt) REVERT: M 1347 MET cc_start: 0.6524 (mtm) cc_final: 0.6142 (mmp) REVERT: R 69 TRP cc_start: 0.6403 (OUTLIER) cc_final: 0.4782 (m100) REVERT: R 238 MET cc_start: 0.8341 (tpp) cc_final: 0.7414 (tpp) REVERT: R 369 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8940 (mm) REVERT: S 278 ARG cc_start: 0.6922 (mmt-90) cc_final: 0.5524 (tpm170) REVERT: U 165 MET cc_start: 0.5986 (mmt) cc_final: 0.5641 (mmm) REVERT: U 193 ASP cc_start: 0.7548 (OUTLIER) cc_final: 0.6827 (p0) REVERT: U 295 ILE cc_start: 0.8792 (OUTLIER) cc_final: 0.8372 (pt) REVERT: U 416 ASN cc_start: 0.8619 (p0) cc_final: 0.7952 (t0) REVERT: V 58 CYS cc_start: 0.8906 (m) cc_final: 0.8622 (m) REVERT: V 315 MET cc_start: 0.8484 (tpt) cc_final: 0.7779 (mmt) REVERT: V 456 LEU cc_start: 0.9124 (pp) cc_final: 0.8650 (tp) REVERT: W 182 GLU cc_start: 0.7669 (OUTLIER) cc_final: 0.7432 (tm-30) REVERT: W 255 LEU cc_start: 0.8711 (mt) cc_final: 0.8030 (tp) REVERT: X 53 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7190 (tm-30) REVERT: X 122 MET cc_start: 0.5224 (ptp) cc_final: 0.4937 (mpp) REVERT: X 315 MET cc_start: 0.3316 (ptm) cc_final: 0.1867 (mmm) REVERT: X 344 MET cc_start: 0.1333 (mmp) cc_final: -0.0366 (tpp) REVERT: Y 109 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.6983 (mp) REVERT: Y 117 LEU cc_start: 0.8510 (tp) cc_final: 0.8075 (tt) REVERT: Y 268 GLU cc_start: 0.5950 (OUTLIER) cc_final: 0.5421 (pt0) REVERT: Y 456 ILE cc_start: -0.1854 (OUTLIER) cc_final: -0.2659 (tp) outliers start: 139 outliers final: 88 residues processed: 471 average time/residue: 0.5594 time to fit residues: 440.6902 Evaluate side-chains 421 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 323 time to evaluate : 4.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 31 LYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 115 SER Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain M residue 695 ASN Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 701 LYS Chi-restraints excluded: chain M residue 718 ILE Chi-restraints excluded: chain M residue 734 LEU Chi-restraints excluded: chain M residue 777 TYR Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1075 VAL Chi-restraints excluded: chain M residue 1085 LEU Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1150 VAL Chi-restraints excluded: chain M residue 1152 TYR Chi-restraints excluded: chain M residue 1200 ASN Chi-restraints excluded: chain M residue 1340 ASP Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 47 LYS Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 69 TRP Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 308 ASP Chi-restraints excluded: chain R residue 369 LEU Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain S residue 193 ASN Chi-restraints excluded: chain S residue 244 CYS Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 230 VAL Chi-restraints excluded: chain T residue 285 ARG Chi-restraints excluded: chain T residue 311 ASP Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 95 ASP Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 121 PHE Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 236 VAL Chi-restraints excluded: chain U residue 295 ILE Chi-restraints excluded: chain U residue 315 ASP Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 264 ASP Chi-restraints excluded: chain V residue 390 VAL Chi-restraints excluded: chain V residue 406 MET Chi-restraints excluded: chain W residue 145 ILE Chi-restraints excluded: chain W residue 182 GLU Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 88 LEU Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 133 ILE Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 359 VAL Chi-restraints excluded: chain X residue 369 ILE Chi-restraints excluded: chain X residue 392 ARG Chi-restraints excluded: chain X residue 435 VAL Chi-restraints excluded: chain Y residue 109 LEU Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 262 THR Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 454 VAL Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 303 optimal weight: 2.9990 chunk 195 optimal weight: 5.9990 chunk 293 optimal weight: 10.0000 chunk 147 optimal weight: 0.2980 chunk 96 optimal weight: 8.9990 chunk 95 optimal weight: 7.9990 chunk 311 optimal weight: 1.9990 chunk 334 optimal weight: 7.9990 chunk 242 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 385 optimal weight: 4.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 42 GLN ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M1070 ASN ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 359 ASN S 106 ASN ** S 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 273 ASN ** T 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 119 GLN ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 245 GLN ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.8938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 45872 Z= 0.277 Angle : 0.731 13.673 63556 Z= 0.375 Chirality : 0.044 0.323 7440 Planarity : 0.005 0.068 6874 Dihedral : 23.506 148.941 9048 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 22.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.93 % Allowed : 24.47 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.97 (0.12), residues: 4633 helix: 0.36 (0.11), residues: 2108 sheet: -0.78 (0.21), residues: 597 loop : -1.69 (0.13), residues: 1928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP M1343 HIS 0.012 0.001 HIS Y 299 PHE 0.052 0.002 PHE M 764 TYR 0.028 0.002 TYR G 86 ARG 0.010 0.001 ARG Y 204 *********************** 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 467 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 310 time to evaluate : 4.477 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7728 (ttp-170) REVERT: B 83 ARG cc_start: 0.7415 (mmt180) cc_final: 0.7021 (mtt180) REVERT: C 92 ARG cc_start: 0.7521 (OUTLIER) cc_final: 0.7206 (ttp80) REVERT: E 57 GLU cc_start: 0.7916 (tt0) cc_final: 0.7627 (tt0) REVERT: G 34 LYS cc_start: 0.4394 (mttp) cc_final: 0.3707 (ptpp) REVERT: G 36 ARG cc_start: 0.5137 (ttt180) cc_final: 0.4631 (mmp80) REVERT: H 105 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7844 (tp) REVERT: M 737 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.8377 (t80) REVERT: M 777 TYR cc_start: 0.5219 (OUTLIER) cc_final: 0.4980 (m-80) REVERT: R 69 TRP cc_start: 0.6556 (OUTLIER) cc_final: 0.4796 (m100) REVERT: R 238 MET cc_start: 0.8216 (tpp) cc_final: 0.7736 (mmm) REVERT: S 278 ARG cc_start: 0.6998 (mmt-90) cc_final: 0.5454 (tpm170) REVERT: U 193 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.6870 (p0) REVERT: U 295 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8484 (pt) REVERT: U 416 ASN cc_start: 0.8739 (p0) cc_final: 0.8122 (t0) REVERT: V 122 MET cc_start: 0.9187 (tmm) cc_final: 0.8318 (tmm) REVERT: V 456 LEU cc_start: 0.9185 (pp) cc_final: 0.8680 (tp) REVERT: W 86 MET cc_start: 0.8005 (tpt) cc_final: 0.7771 (tpt) REVERT: W 169 TYR cc_start: 0.7480 (m-10) cc_final: 0.7261 (m-10) REVERT: W 182 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7391 (tm-30) REVERT: W 255 LEU cc_start: 0.8887 (mt) cc_final: 0.8136 (tp) REVERT: X 53 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7441 (tm-30) REVERT: X 146 GLU cc_start: -0.4208 (OUTLIER) cc_final: -0.4494 (pt0) REVERT: X 236 GLU cc_start: 0.7007 (pm20) cc_final: 0.6783 (pt0) REVERT: X 315 MET cc_start: 0.3273 (ptm) cc_final: 0.2067 (mmp) REVERT: X 387 ARG cc_start: 0.7025 (tpt170) cc_final: 0.6426 (tpt170) REVERT: Y 117 LEU cc_start: 0.8412 (tp) cc_final: 0.7936 (tt) REVERT: Y 268 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6177 (pt0) REVERT: Y 456 ILE cc_start: -0.1879 (OUTLIER) cc_final: -0.3344 (tp) outliers start: 157 outliers final: 116 residues processed: 441 average time/residue: 0.5515 time to fit residues: 406.1100 Evaluate side-chains 410 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 282 time to evaluate : 4.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain G residue 97 ILE Chi-restraints excluded: chain G residue 105 LEU Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain M residue 695 ASN Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 701 LYS Chi-restraints excluded: chain M residue 718 ILE Chi-restraints excluded: chain M residue 734 LEU Chi-restraints excluded: chain M residue 737 TYR Chi-restraints excluded: chain M residue 777 TYR Chi-restraints excluded: chain M residue 858 ASN Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1075 VAL Chi-restraints excluded: chain M residue 1085 LEU Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1150 VAL Chi-restraints excluded: chain M residue 1152 TYR Chi-restraints excluded: chain M residue 1199 LEU Chi-restraints excluded: chain M residue 1200 ASN Chi-restraints excluded: chain M residue 1271 MET Chi-restraints excluded: chain M residue 1340 ASP Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 47 LYS Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 69 TRP Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 186 ASP Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 223 LEU Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 308 ASP Chi-restraints excluded: chain R residue 340 MET Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain S residue 193 ASN Chi-restraints excluded: chain S residue 244 CYS Chi-restraints excluded: chain S residue 251 ASP Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 85 LYS Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 223 ASP Chi-restraints excluded: chain T residue 285 ARG Chi-restraints excluded: chain T residue 311 ASP Chi-restraints excluded: chain T residue 316 LEU Chi-restraints excluded: chain T residue 411 SER Chi-restraints excluded: chain U residue 24 SER Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 57 ILE Chi-restraints excluded: chain U residue 95 ASP Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 121 PHE Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 173 ASN Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 236 VAL Chi-restraints excluded: chain U residue 295 ILE Chi-restraints excluded: chain U residue 315 ASP Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 86 THR Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 90 LEU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 209 VAL Chi-restraints excluded: chain V residue 254 VAL Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 332 ILE Chi-restraints excluded: chain V residue 362 ASP Chi-restraints excluded: chain W residue 145 ILE Chi-restraints excluded: chain W residue 182 GLU Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 238 THR Chi-restraints excluded: chain W residue 251 THR Chi-restraints excluded: chain W residue 305 CYS Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain W residue 367 ILE Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 75 ILE Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 146 GLU Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 359 VAL Chi-restraints excluded: chain X residue 369 ILE Chi-restraints excluded: chain X residue 392 ARG Chi-restraints excluded: chain X residue 397 SER Chi-restraints excluded: chain X residue 435 VAL Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 211 ASP Chi-restraints excluded: chain Y residue 262 THR Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 446 optimal weight: 9.9990 chunk 470 optimal weight: 8.9990 chunk 428 optimal weight: 1.9990 chunk 457 optimal weight: 0.0040 chunk 469 optimal weight: 4.9990 chunk 275 optimal weight: 0.6980 chunk 199 optimal weight: 0.9980 chunk 358 optimal weight: 0.9990 chunk 140 optimal weight: 7.9990 chunk 413 optimal weight: 10.0000 chunk 432 optimal weight: 0.8980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 75 HIS F 42 GLN ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 10 ASN ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 359 ASN S 273 ASN ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 331 ASN ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.8870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 45872 Z= 0.179 Angle : 0.681 16.278 63556 Z= 0.341 Chirality : 0.042 0.363 7440 Planarity : 0.004 0.057 6874 Dihedral : 23.372 149.324 9046 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.73 % Favored : 95.25 % Rotamer: Outliers : 2.86 % Allowed : 25.60 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.12), residues: 4633 helix: 0.65 (0.11), residues: 2121 sheet: -0.71 (0.21), residues: 592 loop : -1.59 (0.14), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP M1343 HIS 0.007 0.001 HIS C 75 PHE 0.030 0.001 PHE V 309 TYR 0.025 0.002 TYR W 169 ARG 0.006 0.001 ARG T 126 *********************** 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 444 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 330 time to evaluate : 4.301 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: 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 131 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.7545 (ttp-170) REVERT: E 57 GLU cc_start: 0.7841 (tt0) cc_final: 0.7566 (tt0) REVERT: F 114 GLN cc_start: 0.7990 (tm-30) cc_final: 0.7669 (tm-30) REVERT: H 105 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7873 (tp) REVERT: M 777 TYR cc_start: 0.5185 (OUTLIER) cc_final: 0.4960 (m-80) REVERT: M 1347 MET cc_start: 0.6919 (OUTLIER) cc_final: 0.6021 (mmp) REVERT: R 69 TRP cc_start: 0.6379 (OUTLIER) cc_final: 0.4761 (m100) REVERT: R 238 MET cc_start: 0.8337 (tpp) cc_final: 0.7734 (tpp) REVERT: S 278 ARG cc_start: 0.6946 (mmt-90) cc_final: 0.5517 (tpm170) REVERT: T 315 MET cc_start: 0.7384 (mmm) cc_final: 0.7052 (mmm) REVERT: U 165 MET cc_start: 0.5675 (mmt) cc_final: 0.5332 (mmm) REVERT: U 193 ASP cc_start: 0.7784 (OUTLIER) cc_final: 0.7148 (p0) REVERT: U 416 ASN cc_start: 0.8740 (p0) cc_final: 0.8131 (t0) REVERT: V 58 CYS cc_start: 0.8684 (m) cc_final: 0.8388 (m) REVERT: V 122 MET cc_start: 0.9106 (tmm) cc_final: 0.8209 (tmm) REVERT: V 456 LEU cc_start: 0.9185 (pp) cc_final: 0.8751 (tp) REVERT: W 86 MET cc_start: 0.7919 (tpt) cc_final: 0.7698 (tpt) REVERT: W 169 TYR cc_start: 0.7541 (m-10) cc_final: 0.7268 (m-10) REVERT: W 255 LEU cc_start: 0.8738 (mt) cc_final: 0.8081 (tp) REVERT: X 53 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7224 (tm-30) REVERT: X 122 MET cc_start: 0.5122 (ptp) cc_final: 0.4873 (mpp) REVERT: X 315 MET cc_start: 0.2961 (ptm) cc_final: 0.1791 (mmp) REVERT: Y 109 LEU cc_start: 0.7393 (OUTLIER) cc_final: 0.6794 (mp) REVERT: Y 117 LEU cc_start: 0.8577 (tp) cc_final: 0.8174 (tt) REVERT: Y 268 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5800 (pt0) REVERT: Y 323 MET cc_start: 0.8011 (tpp) cc_final: 0.7344 (tpp) REVERT: Y 363 GLU cc_start: 0.5611 (mt-10) cc_final: 0.4271 (mm-30) REVERT: Y 455 GLN cc_start: 0.4077 (mp10) cc_final: 0.1127 (tp40) REVERT: Y 456 ILE cc_start: -0.1749 (OUTLIER) cc_final: -0.2101 (tp) outliers start: 114 outliers final: 85 residues processed: 423 average time/residue: 0.5440 time to fit residues: 387.1121 Evaluate side-chains 398 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 304 time to evaluate : 4.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 89 ILE Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain G residue 55 THR Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain H residue 105 LEU Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain M residue 695 ASN Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 701 LYS Chi-restraints excluded: chain M residue 718 ILE Chi-restraints excluded: chain M residue 734 LEU Chi-restraints excluded: chain M residue 777 TYR Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1085 LEU Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1150 VAL Chi-restraints excluded: chain M residue 1199 LEU Chi-restraints excluded: chain M residue 1340 ASP Chi-restraints excluded: chain M residue 1347 MET Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 47 LYS Chi-restraints excluded: chain R residue 63 LEU Chi-restraints excluded: chain R residue 69 TRP Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 308 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain S residue 193 ASN Chi-restraints excluded: chain S residue 244 CYS Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 136 THR Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 311 ASP Chi-restraints excluded: chain T residue 411 SER Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 71 VAL Chi-restraints excluded: chain U residue 95 ASP Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 121 PHE Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 236 VAL Chi-restraints excluded: chain U residue 315 ASP Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 88 LEU Chi-restraints excluded: chain V residue 115 VAL Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain W residue 265 ILE Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain W residue 367 ILE Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 359 VAL Chi-restraints excluded: chain X residue 369 ILE Chi-restraints excluded: chain X residue 392 ARG Chi-restraints excluded: chain X residue 397 SER Chi-restraints excluded: chain Y residue 106 ILE Chi-restraints excluded: chain Y residue 109 LEU Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 175 MET Chi-restraints excluded: chain Y residue 211 ASP Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 455 optimal weight: 0.0770 chunk 300 optimal weight: 0.0010 chunk 483 optimal weight: 8.9990 chunk 295 optimal weight: 0.9980 chunk 229 optimal weight: 0.9990 chunk 336 optimal weight: 10.0000 chunk 507 optimal weight: 1.9990 chunk 466 optimal weight: 10.0000 chunk 403 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 311 optimal weight: 0.9990 overall best weight: 0.6148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6946 moved from start: 0.8922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 45872 Z= 0.172 Angle : 0.666 11.937 63556 Z= 0.334 Chirality : 0.041 0.291 7440 Planarity : 0.004 0.058 6874 Dihedral : 23.206 149.524 9041 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.48 % Allowed : 25.90 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.50 (0.12), residues: 4633 helix: 0.82 (0.12), residues: 2107 sheet: -0.65 (0.21), residues: 596 loop : -1.49 (0.14), residues: 1930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP M1343 HIS 0.007 0.001 HIS U 153 PHE 0.029 0.001 PHE V 309 TYR 0.032 0.002 TYR D 88 ARG 0.008 0.000 ARG T 126 ********************** 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 423 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 324 time to evaluate : 4.495 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: 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 131 ARG cc_start: 0.8030 (OUTLIER) cc_final: 0.7575 (ttp-170) REVERT: E 57 GLU cc_start: 0.7877 (tt0) cc_final: 0.7618 (tt0) REVERT: F 114 GLN cc_start: 0.7955 (tm-30) cc_final: 0.7640 (tm-30) REVERT: H 65 LEU cc_start: 0.9390 (tp) cc_final: 0.9094 (tt) REVERT: M 1343 TRP cc_start: 0.7160 (t60) cc_final: 0.6931 (t60) REVERT: R 238 MET cc_start: 0.8306 (tpp) cc_final: 0.7694 (tpp) REVERT: S 278 ARG cc_start: 0.6956 (mmt-90) cc_final: 0.5515 (tpm170) REVERT: T 232 LEU cc_start: 0.7372 (tt) cc_final: 0.6872 (mm) REVERT: T 315 MET cc_start: 0.7171 (mmm) cc_final: 0.6888 (mmm) REVERT: U 165 MET cc_start: 0.5671 (mmt) cc_final: 0.5335 (mmm) REVERT: U 193 ASP cc_start: 0.7770 (OUTLIER) cc_final: 0.7139 (p0) REVERT: U 416 ASN cc_start: 0.8706 (p0) cc_final: 0.8121 (t0) REVERT: V 58 CYS cc_start: 0.8718 (m) cc_final: 0.8424 (m) REVERT: V 456 LEU cc_start: 0.9209 (pp) cc_final: 0.8781 (tp) REVERT: W 169 TYR cc_start: 0.7605 (m-10) cc_final: 0.7329 (m-10) REVERT: W 255 LEU cc_start: 0.8728 (mt) cc_final: 0.8087 (tp) REVERT: X 53 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7173 (tm-30) REVERT: X 122 MET cc_start: 0.5079 (ptp) cc_final: 0.4492 (ptp) REVERT: X 146 GLU cc_start: -0.3988 (OUTLIER) cc_final: -0.4287 (pt0) REVERT: X 236 GLU cc_start: 0.7174 (OUTLIER) cc_final: 0.6596 (pm20) REVERT: X 315 MET cc_start: 0.3089 (ptm) cc_final: 0.1611 (mmm) REVERT: Y 109 LEU cc_start: 0.7322 (OUTLIER) cc_final: 0.6751 (mp) REVERT: Y 117 LEU cc_start: 0.8580 (tp) cc_final: 0.8230 (tt) REVERT: Y 268 GLU cc_start: 0.6155 (OUTLIER) cc_final: 0.5804 (pt0) REVERT: Y 323 MET cc_start: 0.8195 (tpp) cc_final: 0.7691 (tpp) REVERT: Y 455 GLN cc_start: 0.4297 (mp10) cc_final: 0.1248 (tp40) REVERT: Y 456 ILE cc_start: -0.1532 (OUTLIER) cc_final: -0.1933 (tp) outliers start: 99 outliers final: 79 residues processed: 405 average time/residue: 0.5583 time to fit residues: 380.0349 Evaluate side-chains 391 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 305 time to evaluate : 3.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain C residue 37 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 72 TYR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain D residue 29 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 VAL Chi-restraints excluded: chain D residue 73 THR Chi-restraints excluded: chain E residue 50 VAL Chi-restraints excluded: chain F residue 24 LEU Chi-restraints excluded: chain H residue 43 TYR Chi-restraints excluded: chain H residue 109 LEU Chi-restraints excluded: chain M residue 698 THR Chi-restraints excluded: chain M residue 701 LYS Chi-restraints excluded: chain M residue 718 ILE Chi-restraints excluded: chain M residue 734 LEU Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1085 LEU Chi-restraints excluded: chain M residue 1117 ASP Chi-restraints excluded: chain M residue 1150 VAL Chi-restraints excluded: chain M residue 1340 ASP Chi-restraints excluded: chain M residue 1361 THR Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 47 LYS Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 294 ASN Chi-restraints excluded: chain R residue 308 ASP Chi-restraints excluded: chain S residue 1 MET Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain S residue 193 ASN Chi-restraints excluded: chain S residue 244 CYS Chi-restraints excluded: chain T residue 76 LEU Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 189 ILE Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 311 ASP Chi-restraints excluded: chain T residue 411 SER Chi-restraints excluded: chain U residue 45 VAL Chi-restraints excluded: chain U residue 95 ASP Chi-restraints excluded: chain U residue 106 ILE Chi-restraints excluded: chain U residue 109 LEU Chi-restraints excluded: chain U residue 121 PHE Chi-restraints excluded: chain U residue 167 THR Chi-restraints excluded: chain U residue 193 ASP Chi-restraints excluded: chain U residue 236 VAL Chi-restraints excluded: chain V residue 76 LEU Chi-restraints excluded: chain V residue 118 THR Chi-restraints excluded: chain V residue 304 ILE Chi-restraints excluded: chain V residue 318 ILE Chi-restraints excluded: chain V residue 406 MET Chi-restraints excluded: chain W residue 145 ILE Chi-restraints excluded: chain W residue 183 LYS Chi-restraints excluded: chain W residue 265 ILE Chi-restraints excluded: chain W residue 269 VAL Chi-restraints excluded: chain W residue 360 ASN Chi-restraints excluded: chain W residue 367 ILE Chi-restraints excluded: chain W residue 382 ASP Chi-restraints excluded: chain X residue 33 LEU Chi-restraints excluded: chain X residue 49 VAL Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain X residue 115 VAL Chi-restraints excluded: chain X residue 118 THR Chi-restraints excluded: chain X residue 146 GLU Chi-restraints excluded: chain X residue 236 GLU Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain X residue 268 MET Chi-restraints excluded: chain X residue 337 VAL Chi-restraints excluded: chain X residue 359 VAL Chi-restraints excluded: chain X residue 369 ILE Chi-restraints excluded: chain X residue 392 ARG Chi-restraints excluded: chain X residue 397 SER Chi-restraints excluded: chain Y residue 73 VAL Chi-restraints excluded: chain Y residue 109 LEU Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 211 ASP Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 339 SER Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 247 optimal weight: 10.0000 chunk 320 optimal weight: 1.9990 chunk 430 optimal weight: 0.8980 chunk 123 optimal weight: 9.9990 chunk 372 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 404 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 415 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 42 GLN ** G 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M1352 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 10 ASN ** R 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 155 GLN ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 453 ASN ** 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 = 0.4229 r_free = 0.4229 target = 0.085955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.070447 restraints weight = 348482.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.072021 restraints weight = 209049.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.073040 restraints weight = 142746.291| |-----------------------------------------------------------------------------| r_work (final): 0.3900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.9162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 45872 Z= 0.196 Angle : 0.679 17.000 63556 Z= 0.340 Chirality : 0.041 0.305 7440 Planarity : 0.004 0.057 6874 Dihedral : 23.173 149.560 9040 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.45 % Allowed : 26.05 % Favored : 71.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.47 (0.12), residues: 4633 helix: 0.83 (0.11), residues: 2122 sheet: -0.63 (0.21), residues: 599 loop : -1.49 (0.14), residues: 1912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 760 HIS 0.009 0.001 HIS Y 299 PHE 0.027 0.001 PHE V 309 TYR 0.027 0.002 TYR M 777 ARG 0.009 0.001 ARG T 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10505.45 seconds wall clock time: 193 minutes 50.29 seconds (11630.29 seconds total)