Starting phenix.real_space_refine on Sun Mar 24 23:56:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijj_9678/03_2024/6ijj_9678_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijj_9678/03_2024/6ijj_9678.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijj_9678/03_2024/6ijj_9678_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijj_9678/03_2024/6ijj_9678_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijj_9678/03_2024/6ijj_9678_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijj_9678/03_2024/6ijj_9678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijj_9678/03_2024/6ijj_9678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijj_9678/03_2024/6ijj_9678_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ijj_9678/03_2024/6ijj_9678_updated.pdb" } resolution = 2.89 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 ------------------------------------------------------------------------------- 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= 0.004 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 12 7.16 5 P 14 5.49 5 Mg 216 5.21 5 S 123 5.16 5 C 32049 2.51 5 N 5888 2.21 5 O 6666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 97": "NH1" <-> "NH2" Residue "A ARG 558": "NH1" <-> "NH2" Residue "A ARG 561": "NH1" <-> "NH2" Residue "A ARG 690": "NH1" <-> "NH2" Residue "B TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 397": "NH1" <-> "NH2" Residue "B ARG 411": "NH1" <-> "NH2" Residue "B TYR 636": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 19": "NH1" <-> "NH2" Residue "D ARG 158": "NH1" <-> "NH2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "F ARG 212": "NH1" <-> "NH2" Residue "K ARG 97": "NH1" <-> "NH2" Residue "L ARG 138": "NH1" <-> "NH2" Residue "L ARG 169": "NH1" <-> "NH2" Residue "a ARG 103": "NH1" <-> "NH2" Residue "3 TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 162": "NH1" <-> "NH2" Residue "4 ARG 131": "NH1" <-> "NH2" Residue "4 ARG 189": "NH1" <-> "NH2" Residue "4 ARG 190": "NH1" <-> "NH2" Residue "5 ARG 96": "NH1" <-> "NH2" Residue "5 ARG 152": "NH1" <-> "NH2" Residue "6 ARG 90": "NH1" <-> "NH2" Residue "6 ARG 137": "NH1" <-> "NH2" Residue "6 ARG 188": "NH1" <-> "NH2" Residue "7 ARG 195": "NH1" <-> "NH2" Residue "8 ARG 107": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 44968 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 5819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5819 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 29, 'TRANS': 711} Chain: "B" Number of atoms: 5812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 731, 5812 Classifications: {'peptide': 731} Link IDs: {'PTRANS': 30, 'TRANS': 700} Chain: "C" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 600 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 4, 'TRANS': 75} Chain: "D" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1129 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 12, 'TRANS': 131} Chain: "E" Number of atoms: 505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 505 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 3, 'TRANS': 60} Chain: "F" Number of atoms: 1254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1254 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 9, 'TRANS': 154} Chain: "I" Number of atoms: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 242 Classifications: {'peptide': 32} Link IDs: {'PTRANS': 4, 'TRANS': 27} Chain: "J" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 337 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 3, 'TRANS': 37} Chain: "K" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 578 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "L" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 761 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain breaks: 1 Chain: "1" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1433 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 13, 'TRANS': 179} Chain: "a" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1444 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 13, 'TRANS': 180} Chain: "3" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1683 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 14, 'TRANS': 206} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "4" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1631 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 17, 'TRANS': 192} Chain: "5" Number of atoms: 1765 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1765 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 18, 'TRANS': 207} Chain: "6" Number of atoms: 1771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1771 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 25, 'TRANS': 204} Chain: "7" Number of atoms: 1649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1649 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 15, 'TRANS': 197} Chain: "8" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1630 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 16, 'TRANS': 198} Chain: "A" Number of atoms: 3126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 3126 Unusual residues: {'BCR': 6, 'CLA': 45, 'LHG': 2, 'LMG': 1, 'LMU': 3, 'PQN': 1, 'SF4': 1} Classifications: {'undetermined': 59} Link IDs: {None: 58} Unresolved non-hydrogen bonds: 338 Unresolved non-hydrogen angles: 408 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'CLA:plan-4': 4, 'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 2688 Unusual residues: {'BCR': 7, 'CLA': 40, 'DGD': 1, 'LHG': 1, 'PQN': 1} Classifications: {'undetermined': 50} Link IDs: {None: 49} Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 412 Unresolved non-hydrogen dihedrals: 194 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'CLA:plan-2': 1, 'CLA:plan-4': 6, 'CLA:plan-5': 10} Unresolved non-hydrogen planarities: 61 Chain: "C" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCR': 1, 'CLA': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 67 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'CLA:plan-4': 2, 'CLA:plan-5': 2} Unresolved non-hydrogen planarities: 17 Chain: "J" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'BCR': 1, 'CLA': 1, 'DGD': 1, 'LMG': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CLA:plan-4': 1, 'CLA:plan-5': 1} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 316 Unusual residues: {'BCR': 2, 'CLA': 4, 'LMU': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'CLA:plan-5': 3} Unresolved non-hydrogen planarities: 14 Chain: "L" Number of atoms: 215 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 215 Unusual residues: {'BCR': 2, 'CLA': 3} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'CLA:plan-5': 3} Unresolved non-hydrogen planarities: 15 Chain: "1" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 850 Unusual residues: {'BCR': 1, 'CLA': 14, 'LHG': 1, 'LUT': 1, 'XAT': 1} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 125 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'CLA:plan-2': 3, 'CLA:plan-3': 1, 'CLA:plan-4': 5, 'CLA:plan-5': 8} Unresolved non-hydrogen planarities: 65 Chain: "a" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 897 Unusual residues: {'BCR': 1, 'CLA': 14, 'LHG': 1, 'LUT': 1, 'XAT': 1} Classifications: {'undetermined': 18} Link IDs: {None: 17} Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'CLA:plan-2': 1, 'CLA:plan-3': 1, 'CLA:plan-4': 2, 'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 38 Chain: "3" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1024 Unusual residues: {'BCR': 3, 'CLA': 14, 'LHG': 2, 'LUT': 1, 'XAT': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 190 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'CLA:plan-2': 2, 'CLA:plan-4': 6, 'CLA:plan-5': 5} Unresolved non-hydrogen planarities: 45 Chain: "4" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1037 Unusual residues: {'BCR': 1, 'CLA': 15, 'LHG': 1, 'LMG': 2, 'LUT': 1, 'XAT': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'CLA:plan-2': 4, 'CLA:plan-4': 4, 'CLA:plan-5': 7} Unresolved non-hydrogen planarities: 51 Chain: "5" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 1259 Unusual residues: {'BCR': 1, 'CLA': 17, 'LHG': 2, 'LMG': 2, 'LMU': 1, 'LUT': 1, 'NEX': 1, 'XAT': 1} Classifications: {'undetermined': 26} Link IDs: {None: 25} Unresolved non-hydrogen bonds: 259 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 23 Planarities with less than four sites: {'CLA:plan-2': 5, 'CLA:plan-3': 1, 'CLA:plan-4': 5, 'CLA:plan-5': 7} Unresolved non-hydrogen planarities: 54 Chain: "6" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 1111 Unusual residues: {'BCR': 1, 'CLA': 17, 'LHG': 1, 'LUT': 1, 'NEX': 1, 'XAT': 1} Classifications: {'undetermined': 22} Link IDs: {None: 21} Unresolved non-hydrogen bonds: 213 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'CLA:plan-2': 3, 'CLA:plan-4': 5, 'CLA:plan-5': 8} Unresolved non-hydrogen planarities: 58 Chain: "7" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1005 Unusual residues: {'BCR': 2, 'CLA': 15, 'LHG': 1, 'LMG': 1, 'LUT': 1, 'XAT': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 240 Unresolved non-hydrogen angles: 285 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'CLA:plan-2': 2, 'CLA:plan-3': 1, 'CLA:plan-4': 4, 'CLA:plan-5': 8} Unresolved non-hydrogen planarities: 56 Chain: "8" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 1021 Unusual residues: {'BCR': 1, 'CLA': 14, 'LHG': 2, 'LMU': 2, 'LUT': 1, 'XAT': 1} Classifications: {'undetermined': 21} Link IDs: {None: 20} Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 220 Unresolved non-hydrogen dihedrals: 103 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'CLA:plan-2': 3, 'CLA:plan-4': 3, 'CLA:plan-5': 6} Unresolved non-hydrogen planarities: 42 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10248 SG CYS B 569 66.959 52.374 91.071 1.00 24.73 S ATOM 4443 SG CYS A 575 70.055 48.272 95.651 1.00 24.48 S ATOM 11751 SG CYS C 17 85.625 38.249 93.474 1.00 38.87 S Time building chain proxies: 22.28, per 1000 atoms: 0.50 Number of scatterers: 44968 At special positions: 0 Unit cell: (135.2, 173.68, 185.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 12 26.01 S 123 16.00 P 14 15.00 Mg 216 11.99 O 6666 8.00 N 5888 7.00 C 32049 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS F 70 " - pdb=" SG CYS F 125 " distance=2.03 Simple disulfide: pdb=" SG CYS 5 251 " - pdb=" SG CYS 5 268 " distance=2.04 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 Atom "HETATM38507 O6 LHG a 620 .*. O " rejected from bonding due to valence issues. Atom "HETATM37610 O6 LHG 1 620 .*. O " rejected from bonding due to valence issues. Atom "HETATM41621 O6 LHG 5 623 .*. O " rejected from bonding due to valence issues. Atom "HETATM40488 O6 LHG 4 622 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=157, symmetry=0 Number of additional bonds: simple=157, symmetry=0 Coordination: Other bonds: Time building additional restraints: 19.42 Conformation dependent library (CDL) restraints added in 5.7 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A 853 " pdb="FE4 SF4 A 853 " - pdb=" SG CYS A 575 " pdb="FE3 SF4 A 853 " - pdb=" SG CYS B 569 " pdb="FE1 SF4 A 853 " - pdb=" SG CYS B 560 " pdb="FE2 SF4 A 853 " - pdb=" SG CYS A 584 " pdb=" SF4 C 101 " pdb="FE3 SF4 C 101 " - pdb=" SG CYS C 21 " pdb="FE4 SF4 C 101 " - pdb=" SG CYS C 48 " pdb="FE2 SF4 C 101 " - pdb=" SG CYS C 51 " pdb="FE1 SF4 C 101 " - pdb=" SG CYS C 54 " pdb=" SF4 C 102 " pdb="FE2 SF4 C 102 " - pdb=" SG CYS C 17 " pdb="FE4 SF4 C 102 " - pdb=" SG CYS C 11 " pdb="FE3 SF4 C 102 " - pdb=" SG CYS C 14 " pdb="FE1 SF4 C 102 " - pdb=" SG CYS C 58 " Number of angles added : 36 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6948 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 143 helices and 13 sheets defined 50.7% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.29 Creating SS restraints... Processing helix chain 'A' and resid 39 through 41 No H-bonds generated for 'chain 'A' and resid 39 through 41' Processing helix chain 'A' and resid 47 through 54 removed outlier: 3.762A pdb=" N HIS A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 62 No H-bonds generated for 'chain 'A' and resid 59 through 62' Processing helix chain 'A' and resid 66 through 97 removed outlier: 3.520A pdb=" N HIS A 77 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE A 78 " --> pdb=" O PHE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 104 No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'A' and resid 124 through 127 Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 156 through 182 Processing helix chain 'A' and resid 188 through 191 No H-bonds generated for 'chain 'A' and resid 188 through 191' Processing helix chain 'A' and resid 194 through 203 Processing helix chain 'A' and resid 206 through 219 Processing helix chain 'A' and resid 221 through 230 Processing helix chain 'A' and resid 240 through 245 Processing helix chain 'A' and resid 247 through 253 Processing helix chain 'A' and resid 257 through 265 removed outlier: 6.970A pdb=" N ILE A 261 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 262 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Proline residue: A 263 - end of helix Processing helix chain 'A' and resid 269 through 274 removed outlier: 4.182A pdb=" N ASP A 274 " --> pdb=" O GLU A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 310 removed outlier: 3.887A pdb=" N HIS A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 326 Processing helix chain 'A' and resid 341 through 344 No H-bonds generated for 'chain 'A' and resid 341 through 344' Processing helix chain 'A' and resid 349 through 373 removed outlier: 3.673A pdb=" N ILE A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR A 372 " --> pdb=" O ALA A 368 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ALA A 373 " --> pdb=" O HIS A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 414 removed outlier: 3.660A pdb=" N ALA A 410 " --> pdb=" O GLY A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 464 removed outlier: 3.510A pdb=" N HIS A 433 " --> pdb=" O ARG A 429 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASP A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ALA A 436 " --> pdb=" O ARG A 432 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N LEU A 455 " --> pdb=" O HIS A 451 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 482 through 492 Processing helix chain 'A' and resid 494 through 497 No H-bonds generated for 'chain 'A' and resid 494 through 497' Processing helix chain 'A' and resid 530 through 555 Processing helix chain 'A' and resid 566 through 569 No H-bonds generated for 'chain 'A' and resid 566 through 569' Processing helix chain 'A' and resid 588 through 617 removed outlier: 3.831A pdb=" N PHE A 597 " --> pdb=" O PHE A 593 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TRP A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE A 605 " --> pdb=" O ASN A 601 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN A 615 " --> pdb=" O SER A 611 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 638 No H-bonds generated for 'chain 'A' and resid 635 through 638' Processing helix chain 'A' and resid 642 through 647 Processing helix chain 'A' and resid 650 through 656 removed outlier: 3.793A pdb=" N SER A 655 " --> pdb=" O TRP A 651 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N GLN A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 664 through 687 removed outlier: 4.387A pdb=" N ALA A 667 " --> pdb=" O ALA A 664 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ILE A 671 " --> pdb=" O TYR A 668 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE A 672 " --> pdb=" O GLY A 669 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ALA A 675 " --> pdb=" O PHE A 672 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL A 678 " --> pdb=" O ALA A 675 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TRP A 679 " --> pdb=" O HIS A 676 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU A 686 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE A 687 " --> pdb=" O MET A 684 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 706 removed outlier: 3.807A pdb=" N GLU A 695 " --> pdb=" O GLY A 691 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 750 removed outlier: 3.656A pdb=" N ALA A 725 " --> pdb=" O THR A 721 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N SER A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 40 through 72 Processing helix chain 'B' and resid 75 through 80 removed outlier: 3.732A pdb=" N THR B 80 " --> pdb=" O GLU B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 Processing helix chain 'B' and resid 121 through 126 Processing helix chain 'B' and resid 134 through 158 removed outlier: 3.611A pdb=" N VAL B 138 " --> pdb=" O GLN B 134 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B 139 " --> pdb=" O ASP B 135 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LEU B 158 " --> pdb=" O GLY B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 169 No H-bonds generated for 'chain 'B' and resid 166 through 169' Processing helix chain 'B' and resid 172 through 181 removed outlier: 3.576A pdb=" N LEU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 197 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 231 through 235 Processing helix chain 'B' and resid 271 through 290 Processing helix chain 'B' and resid 302 through 308 removed outlier: 4.021A pdb=" N LEU B 306 " --> pdb=" O MET B 302 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLU B 307 " --> pdb=" O GLN B 303 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 308 " --> pdb=" O ALA B 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 302 through 308' Processing helix chain 'B' and resid 324 through 327 No H-bonds generated for 'chain 'B' and resid 324 through 327' Processing helix chain 'B' and resid 331 through 355 removed outlier: 3.753A pdb=" N TYR B 354 " --> pdb=" O ALA B 350 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER B 355 " --> pdb=" O GLN B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 397 removed outlier: 3.655A pdb=" N PHE B 388 " --> pdb=" O MET B 384 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE B 395 " --> pdb=" O GLY B 391 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 396 " --> pdb=" O ALA B 392 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 414 removed outlier: 3.896A pdb=" N LEU B 413 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 446 Processing helix chain 'B' and resid 450 through 452 No H-bonds generated for 'chain 'B' and resid 450 through 452' Processing helix chain 'B' and resid 459 through 468 removed outlier: 3.600A pdb=" N ILE B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 490 removed outlier: 4.373A pdb=" N GLY B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 495 through 502 Processing helix chain 'B' and resid 515 through 540 Processing helix chain 'B' and resid 551 through 554 No H-bonds generated for 'chain 'B' and resid 551 through 554' Processing helix chain 'B' and resid 574 through 604 removed outlier: 3.591A pdb=" N LEU B 579 " --> pdb=" O ASP B 575 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 580 " --> pdb=" O ALA B 576 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE B 582 " --> pdb=" O TYR B 578 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TRP B 583 " --> pdb=" O LEU B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 607 through 611 Processing helix chain 'B' and resid 617 through 622 Processing helix chain 'B' and resid 625 through 628 No H-bonds generated for 'chain 'B' and resid 625 through 628' Processing helix chain 'B' and resid 633 through 635 No H-bonds generated for 'chain 'B' and resid 633 through 635' Processing helix chain 'B' and resid 645 through 665 removed outlier: 3.519A pdb=" N LEU B 652 " --> pdb=" O ALA B 648 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 659 " --> pdb=" O HIS B 655 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N MET B 663 " --> pdb=" O ALA B 659 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 664 " --> pdb=" O THR B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 671 through 685 removed outlier: 3.549A pdb=" N THR B 678 " --> pdb=" O GLU B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 731 Processing helix chain 'C' and resid 16 through 20 Processing helix chain 'D' and resid 127 through 131 Processing helix chain 'D' and resid 169 through 182 Processing helix chain 'D' and resid 226 through 228 No H-bonds generated for 'chain 'D' and resid 226 through 228' Processing helix chain 'F' and resid 74 through 93 removed outlier: 4.808A pdb=" N GLN F 93 " --> pdb=" O LYS F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 120 Processing helix chain 'F' and resid 152 through 175 removed outlier: 4.057A pdb=" N LEU F 157 " --> pdb=" O THR F 153 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N VAL F 159 " --> pdb=" O GLY F 155 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG F 168 " --> pdb=" O GLY F 164 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL F 174 " --> pdb=" O TYR F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 185 removed outlier: 3.936A pdb=" N ILE F 185 " --> pdb=" O ASP F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 189 through 197 Processing helix chain 'F' and resid 202 through 210 Processing helix chain 'I' and resid 79 through 85 removed outlier: 3.867A pdb=" N GLY I 84 " --> pdb=" O VAL I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 87 through 97 removed outlier: 3.585A pdb=" N LEU I 95 " --> pdb=" O ALA I 91 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N PHE I 96 " --> pdb=" O MET I 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 8 Processing helix chain 'J' and resid 11 through 32 removed outlier: 3.628A pdb=" N THR J 20 " --> pdb=" O THR J 16 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU J 26 " --> pdb=" O THR J 22 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU J 28 " --> pdb=" O GLY J 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 97 removed outlier: 3.567A pdb=" N ALA K 91 " --> pdb=" O ALA K 87 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR K 92 " --> pdb=" O SER K 88 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG K 97 " --> pdb=" O LEU K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 133 through 157 Processing helix chain 'L' and resid 130 through 132 No H-bonds generated for 'chain 'L' and resid 130 through 132' Processing helix chain 'L' and resid 143 through 165 removed outlier: 4.241A pdb=" N PHE L 156 " --> pdb=" O LEU L 152 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N LEU L 157 " --> pdb=" O ALA L 153 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY L 160 " --> pdb=" O PHE L 156 " (cutoff:3.500A) Proline residue: L 161 - end of helix removed outlier: 3.710A pdb=" N LEU L 165 " --> pdb=" O PRO L 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 175 through 201 removed outlier: 3.719A pdb=" N SER L 180 " --> pdb=" O GLU L 176 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ALA L 183 " --> pdb=" O GLY L 179 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 249 removed outlier: 3.590A pdb=" N SER L 230 " --> pdb=" O ALA L 226 " (cutoff:3.500A) Processing helix chain '1' and resid 88 through 118 removed outlier: 3.629A pdb=" N ARG 1 93 " --> pdb=" O ALA 1 89 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL 1 99 " --> pdb=" O THR 1 95 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ILE 1 100 " --> pdb=" O GLU 1 96 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N VAL 1 115 " --> pdb=" O GLY 1 111 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU 1 116 " --> pdb=" O SER 1 112 " (cutoff:3.500A) Processing helix chain '1' and resid 125 through 127 No H-bonds generated for 'chain '1' and resid 125 through 127' Processing helix chain '1' and resid 147 through 156 Processing helix chain '1' and resid 159 through 166 removed outlier: 4.388A pdb=" N GLN 1 164 " --> pdb=" O ALA 1 160 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 218 Processing helix chain '1' and resid 222 through 231 removed outlier: 4.475A pdb=" N GLU 1 228 " --> pdb=" O ALA 1 224 " (cutoff:3.500A) Processing helix chain 'a' and resid 88 through 118 removed outlier: 3.524A pdb=" N GLU a 96 " --> pdb=" O LYS a 92 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL a 99 " --> pdb=" O THR a 95 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL a 115 " --> pdb=" O GLY a 111 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU a 116 " --> pdb=" O SER a 112 " (cutoff:3.500A) Processing helix chain 'a' and resid 125 through 127 No H-bonds generated for 'chain 'a' and resid 125 through 127' Processing helix chain 'a' and resid 147 through 157 Processing helix chain 'a' and resid 159 through 166 removed outlier: 4.168A pdb=" N GLN a 164 " --> pdb=" O ALA a 160 " (cutoff:3.500A) Processing helix chain 'a' and resid 190 through 218 Processing helix chain 'a' and resid 222 through 231 removed outlier: 4.295A pdb=" N GLU a 228 " --> pdb=" O ALA a 224 " (cutoff:3.500A) Processing helix chain '3' and resid 80 through 82 No H-bonds generated for 'chain '3' and resid 80 through 82' Processing helix chain '3' and resid 84 through 113 removed outlier: 3.904A pdb=" N ILE 3 106 " --> pdb=" O ALA 3 102 " (cutoff:3.500A) Proline residue: 3 108 - end of helix Processing helix chain '3' and resid 119 through 121 No H-bonds generated for 'chain '3' and resid 119 through 121' Processing helix chain '3' and resid 125 through 127 No H-bonds generated for 'chain '3' and resid 125 through 127' Processing helix chain '3' and resid 144 through 167 removed outlier: 3.986A pdb=" N ARG 3 161 " --> pdb=" O PHE 3 157 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP 3 165 " --> pdb=" O ARG 3 161 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE 3 166 " --> pdb=" O ARG 3 162 " (cutoff:3.500A) Processing helix chain '3' and resid 180 through 185 removed outlier: 4.153A pdb=" N LYS 3 185 " --> pdb=" O ALA 3 182 " (cutoff:3.500A) Processing helix chain '3' and resid 207 through 238 removed outlier: 4.311A pdb=" N GLN 3 234 " --> pdb=" O GLY 3 230 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET 3 237 " --> pdb=" O ALA 3 233 " (cutoff:3.500A) Processing helix chain '3' and resid 242 through 251 Processing helix chain '3' and resid 259 through 261 No H-bonds generated for 'chain '3' and resid 259 through 261' Processing helix chain '4' and resid 116 through 149 removed outlier: 4.018A pdb=" N TRP 4 121 " --> pdb=" O VAL 4 117 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL 4 142 " --> pdb=" O ALA 4 138 " (cutoff:3.500A) Proline residue: 4 143 - end of helix Processing helix chain '4' and resid 172 through 195 removed outlier: 3.867A pdb=" N ALA 4 184 " --> pdb=" O MET 4 180 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE 4 188 " --> pdb=" O ALA 4 184 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP 4 193 " --> pdb=" O ARG 4 189 " (cutoff:3.500A) Processing helix chain '4' and resid 222 through 224 No H-bonds generated for 'chain '4' and resid 222 through 224' Processing helix chain '4' and resid 234 through 260 Processing helix chain '4' and resid 266 through 275 removed outlier: 3.635A pdb=" N LEU 4 270 " --> pdb=" O PRO 4 266 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N THR 4 272 " --> pdb=" O LYS 4 268 " (cutoff:3.500A) Processing helix chain '4' and resid 282 through 289 Processing helix chain '5' and resid 81 through 111 removed outlier: 3.510A pdb=" N TRP 5 86 " --> pdb=" O THR 5 82 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL 5 107 " --> pdb=" O ALA 5 103 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU 5 109 " --> pdb=" O VAL 5 105 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ILE 5 110 " --> pdb=" O LEU 5 106 " (cutoff:3.500A) Processing helix chain '5' and resid 119 through 121 No H-bonds generated for 'chain '5' and resid 119 through 121' Processing helix chain '5' and resid 128 through 130 No H-bonds generated for 'chain '5' and resid 128 through 130' Processing helix chain '5' and resid 135 through 158 removed outlier: 3.876A pdb=" N VAL 5 149 " --> pdb=" O LEU 5 145 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL 5 151 " --> pdb=" O HIS 5 147 " (cutoff:3.500A) Processing helix chain '5' and resid 196 through 222 removed outlier: 3.639A pdb=" N ALA 5 221 " --> pdb=" O PHE 5 217 " (cutoff:3.500A) Processing helix chain '5' and resid 228 through 237 Processing helix chain '6' and resid 122 through 152 removed outlier: 3.692A pdb=" N LYS 6 126 " --> pdb=" O ALA 6 122 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TRP 6 127 " --> pdb=" O GLU 6 123 " (cutoff:3.500A) Processing helix chain '6' and resid 171 through 194 removed outlier: 3.780A pdb=" N LEU 6 175 " --> pdb=" O PRO 6 171 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL 6 185 " --> pdb=" O LEU 6 181 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL 6 187 " --> pdb=" O HIS 6 183 " (cutoff:3.500A) Processing helix chain '6' and resid 230 through 255 removed outlier: 3.822A pdb=" N ILE 6 238 " --> pdb=" O LYS 6 234 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL 6 249 " --> pdb=" O MET 6 245 " (cutoff:3.500A) Processing helix chain '6' and resid 264 through 271 Processing helix chain '6' and resid 273 through 275 No H-bonds generated for 'chain '6' and resid 273 through 275' Processing helix chain '6' and resid 278 through 281 No H-bonds generated for 'chain '6' and resid 278 through 281' Processing helix chain '7' and resid 62 through 92 removed outlier: 3.623A pdb=" N GLN 7 70 " --> pdb=" O LYS 7 66 " (cutoff:3.500A) Processing helix chain '7' and resid 105 through 111 removed outlier: 3.716A pdb=" N VAL 7 109 " --> pdb=" O ALA 7 105 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL 7 110 " --> pdb=" O GLY 7 106 " (cutoff:3.500A) Processing helix chain '7' and resid 117 through 139 removed outlier: 3.661A pdb=" N ARG 7 135 " --> pdb=" O ALA 7 131 " (cutoff:3.500A) Processing helix chain '7' and resid 167 through 170 No H-bonds generated for 'chain '7' and resid 167 through 170' Processing helix chain '7' and resid 180 through 210 removed outlier: 3.751A pdb=" N ALA 7 205 " --> pdb=" O CYS 7 201 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA 7 206 " --> pdb=" O LEU 7 202 " (cutoff:3.500A) Processing helix chain '7' and resid 215 through 224 removed outlier: 3.578A pdb=" N ALA 7 220 " --> pdb=" O LEU 7 216 " (cutoff:3.500A) Processing helix chain '7' and resid 231 through 233 No H-bonds generated for 'chain '7' and resid 231 through 233' Processing helix chain '8' and resid 67 through 69 No H-bonds generated for 'chain '8' and resid 67 through 69' Processing helix chain '8' and resid 72 through 75 No H-bonds generated for 'chain '8' and resid 72 through 75' Processing helix chain '8' and resid 92 through 124 removed outlier: 3.653A pdb=" N GLN 8 100 " --> pdb=" O ARG 8 96 " (cutoff:3.500A) Proline residue: 8 119 - end of helix Processing helix chain '8' and resid 148 through 171 removed outlier: 3.686A pdb=" N VAL 8 162 " --> pdb=" O LEU 8 158 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS 8 165 " --> pdb=" O PHE 8 161 " (cutoff:3.500A) Processing helix chain '8' and resid 185 through 188 Processing helix chain '8' and resid 200 through 202 No H-bonds generated for 'chain '8' and resid 200 through 202' Processing helix chain '8' and resid 214 through 242 removed outlier: 3.820A pdb=" N THR 8 242 " --> pdb=" O GLN 8 238 " (cutoff:3.500A) Processing helix chain '8' and resid 246 through 255 Processing sheet with id= A, first strand: chain 'A' and resid 17 through 19 Processing sheet with id= B, first strand: chain 'A' and resid 515 through 517 removed outlier: 3.501A pdb=" N MET A 523 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL A 517 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VAL A 521 " --> pdb=" O VAL A 517 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 4 through 7 Processing sheet with id= D, first strand: chain 'C' and resid 26 through 30 Processing sheet with id= E, first strand: chain 'D' and resid 135 through 141 removed outlier: 3.568A pdb=" N TRP D 139 " --> pdb=" O ASN D 162 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'D' and resid 145 through 148 Processing sheet with id= G, first strand: chain 'D' and resid 190 through 192 Processing sheet with id= H, first strand: chain 'E' and resid 139 through 141 removed outlier: 7.021A pdb=" N VAL E 118 " --> pdb=" O VAL E 106 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'K' and resid 106 through 108 Processing sheet with id= J, first strand: chain '1' and resid 136 through 138 removed outlier: 4.002A pdb=" N ALA 1 136 " --> pdb=" O VAL 1 143 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'a' and resid 136 through 138 removed outlier: 4.151A pdb=" N ALA a 136 " --> pdb=" O VAL a 143 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain '5' and resid 257 through 259 removed outlier: 4.113A pdb=" N VAL 5 257 " --> pdb=" O ILE 5 264 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE 5 264 " --> pdb=" O VAL 5 257 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain '6' and resid 283 through 285 1329 hydrogen bonds defined for protein. 3885 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 12.51 Time building geometry restraints manager: 20.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 16452 1.38 - 1.57: 30124 1.57 - 1.75: 42 1.75 - 1.94: 191 1.94 - 2.12: 900 Bond restraints: 47709 Sorted by residual: bond pdb=" C33 NEX 5 624 " pdb=" C34 NEX 5 624 " ideal model delta sigma weight residual 2.765 1.336 1.429 2.00e-02 2.50e+03 5.11e+03 bond pdb=" C33 NEX 6 624 " pdb=" C34 NEX 6 624 " ideal model delta sigma weight residual 2.765 1.339 1.426 2.00e-02 2.50e+03 5.08e+03 bond pdb=" C29 NEX 5 624 " pdb=" C39 NEX 5 624 " ideal model delta sigma weight residual 2.347 1.495 0.852 2.00e-02 2.50e+03 1.82e+03 bond pdb=" C29 NEX 6 624 " pdb=" C39 NEX 6 624 " ideal model delta sigma weight residual 2.347 1.499 0.848 2.00e-02 2.50e+03 1.80e+03 bond pdb=" C10 NEX 5 624 " pdb=" C11 NEX 5 624 " ideal model delta sigma weight residual 2.048 1.455 0.593 2.00e-02 2.50e+03 8.80e+02 ... (remaining 47704 not shown) Histogram of bond angle deviations from ideal: 57.00 - 81.15: 54 81.15 - 105.29: 2485 105.29 - 129.43: 63237 129.43 - 153.57: 1984 153.57 - 177.71: 434 Bond angle restraints: 68194 Sorted by residual: angle pdb=" C11 LUT 4 619 " pdb=" C10 LUT 4 619 " pdb=" C9 LUT 4 619 " ideal model delta sigma weight residual 85.87 126.55 -40.68 3.00e+00 1.11e-01 1.84e+02 angle pdb=" C29 LUT 5 620 " pdb=" C30 LUT 5 620 " pdb=" C31 LUT 5 620 " ideal model delta sigma weight residual 85.90 126.44 -40.54 3.00e+00 1.11e-01 1.83e+02 angle pdb=" C11 LUT 7 619 " pdb=" C10 LUT 7 619 " pdb=" C9 LUT 7 619 " ideal model delta sigma weight residual 85.87 126.37 -40.50 3.00e+00 1.11e-01 1.82e+02 angle pdb=" C11 LUT 6 619 " pdb=" C12 LUT 6 619 " pdb=" C13 LUT 6 619 " ideal model delta sigma weight residual 85.87 126.36 -40.49 3.00e+00 1.11e-01 1.82e+02 angle pdb=" C11 LUT 8 619 " pdb=" C10 LUT 8 619 " pdb=" C9 LUT 8 619 " ideal model delta sigma weight residual 85.87 126.34 -40.47 3.00e+00 1.11e-01 1.82e+02 ... (remaining 68189 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.24: 19751 25.24 - 50.47: 1581 50.47 - 75.71: 513 75.71 - 100.94: 151 100.94 - 126.18: 109 Dihedral angle restraints: 22105 sinusoidal: 11163 harmonic: 10942 Sorted by residual: dihedral pdb=" CA VAL 3 47 " pdb=" C VAL 3 47 " pdb=" N GLY 3 48 " pdb=" CA GLY 3 48 " ideal model delta harmonic sigma weight residual -180.00 -153.48 -26.52 0 5.00e+00 4.00e-02 2.81e+01 dihedral pdb=" CA ALA 8 127 " pdb=" C ALA 8 127 " pdb=" N LEU 8 128 " pdb=" CA LEU 8 128 " ideal model delta harmonic sigma weight residual 180.00 154.15 25.85 0 5.00e+00 4.00e-02 2.67e+01 dihedral pdb=" CA LEU 3 61 " pdb=" C LEU 3 61 " pdb=" N PRO 3 62 " pdb=" CA PRO 3 62 " ideal model delta harmonic sigma weight residual -180.00 -154.38 -25.62 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 22102 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.132: 5578 1.132 - 2.265: 14 2.265 - 3.397: 0 3.397 - 4.529: 0 4.529 - 5.662: 10 Chirality restraints: 5602 Sorted by residual: chirality pdb=" C5 NEX 5 624 " pdb=" C18 NEX 5 624 " pdb=" C4 NEX 5 624 " pdb=" C6 NEX 5 624 " both_signs ideal model delta sigma weight residual False 2.95 -2.71 5.66 2.00e-01 2.50e+01 8.01e+02 chirality pdb=" C5 NEX 6 624 " pdb=" C18 NEX 6 624 " pdb=" C4 NEX 6 624 " pdb=" C6 NEX 6 624 " both_signs ideal model delta sigma weight residual False 2.95 -2.64 5.59 2.00e-01 2.50e+01 7.81e+02 chirality pdb=" C26 LUT 1 617 " pdb=" C21 LUT 1 617 " pdb=" C25 LUT 1 617 " pdb=" C27 LUT 1 617 " both_signs ideal model delta sigma weight residual False -2.77 2.52 -5.30 2.00e-01 2.50e+01 7.02e+02 ... (remaining 5599 not shown) Planarity restraints: 8996 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 NEX 6 624 " 0.057 2.00e-02 2.50e+03 3.05e-01 1.40e+03 pdb=" C5 NEX 6 624 " 0.176 2.00e-02 2.50e+03 pdb=" C6 NEX 6 624 " 0.001 2.00e-02 2.50e+03 pdb=" C7 NEX 6 624 " -0.208 2.00e-02 2.50e+03 pdb=" C8 NEX 6 624 " -0.504 2.00e-02 2.50e+03 pdb=" C9 NEX 6 624 " 0.477 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 NEX 5 624 " -0.048 2.00e-02 2.50e+03 2.20e-01 7.25e+02 pdb=" C5 NEX 5 624 " 0.161 2.00e-02 2.50e+03 pdb=" C6 NEX 5 624 " 0.049 2.00e-02 2.50e+03 pdb=" C7 NEX 5 624 " -0.130 2.00e-02 2.50e+03 pdb=" C8 NEX 5 624 " -0.364 2.00e-02 2.50e+03 pdb=" C9 NEX 5 624 " 0.332 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C11 PQN A 844 " -0.099 2.00e-02 2.50e+03 2.20e-01 6.06e+02 pdb=" C12 PQN A 844 " 0.264 2.00e-02 2.50e+03 pdb=" C13 PQN A 844 " -0.369 2.00e-02 2.50e+03 pdb=" C14 PQN A 844 " 0.157 2.00e-02 2.50e+03 pdb=" C15 PQN A 844 " 0.047 2.00e-02 2.50e+03 ... (remaining 8993 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 540 2.63 - 3.20: 33739 3.20 - 3.76: 79424 3.76 - 4.33: 109174 4.33 - 4.90: 175617 Nonbonded interactions: 398494 Sorted by model distance: nonbonded pdb=" CE1 HIS 8 105 " pdb="MG CLA 8 603 " model vdw 2.060 3.130 nonbonded pdb=" NC CLA 3 611 " pdb=" O4 LHG 3 624 " model vdw 2.213 3.120 nonbonded pdb="MG CLA 3 611 " pdb=" O4 LHG 3 624 " model vdw 2.221 2.910 nonbonded pdb=" OH TYR B 359 " pdb=" OBD CLA B 828 " model vdw 2.233 2.440 nonbonded pdb=" OD1 ASP K 127 " pdb=" NA CLA K 201 " model vdw 2.234 3.120 ... (remaining 398489 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 '1' and (resid 55 through 247 or resid 601 through 610 or (resid 611 and \ (name NB or name ND or name C1A or name C1B or name C1C or name C1D or name C2A \ or name C2B or name C2C or name C2D or name C3A or name C3B or name C3C or name \ C3D or name C4A or name C4B or name C4C or name C4D or name CAA or name CAB or n \ ame CAC or name CAD or name CBD or name CGD or name CHA or name CHB or name CHC \ or name CHD or name CMA or name CMB or name CMC or name CMD or name NA or name N \ C or name O1D or name O2D or name OBD or name MG )) or resid 612 through 620)) selection = (chain 'a' and (resid 55 through 247 or resid 601 through 604 or (resid 606 and \ (name NB or name ND or name C1A or name C1B or name C1C or name C1D or name C2A \ or name C2B or name C2C or name C2D or name C3A or name C3B or name C3C or name \ C3D or name C4A or name C4B or name C4C or name C4D or name CAB or name CAC or n \ ame CAD or name CBB or name CBC or name CBD or name CED or name CGD or name CHA \ or name CHB or name CHC or name CHD or name CMA or name CMB or name CMC or name \ CMD or name NA or name NC or name O2D or name OBD or name MG )) or (resid 607 an \ d (name NB or name ND or name C1A or name C1B or name C1C or name C1D or name C2 \ A or name C2B or name C2C or name C2D or name C3A or name C3B or name C3C or nam \ e C3D or name C4A or name C4B or name C4C or name C4D or name CAA or name CAB or \ name CAC or name CAD or name CBB or name CBC or name CBD or name CGD or name CH \ A or name CHB or name CHC or name CHD or name CMA or name CMB or name CMC or nam \ e CMD or name NA or name NC or name O1D or name O2D or name OBD or name MG )) or \ resid 608 or (resid 609 and (name NB or name ND or name C1A or name C1B or name \ C1C or name C1D or name C2A or name C2B or name C2C or name C2D or name C3A or \ name C3B or name C3C or name C3D or name C4A or name C4B or name C4C or name C4D \ or name CAA or name CAB or name CAC or name CAD or name CBC or name CBD or name \ CED or name CGD or name CHA or name CHB or name CHC or name CHD or name CMA or \ name CMB or name CMC or name CMD or name NA or name NC or name O1D or name O2D o \ r name OBD or name MG )) or (resid 610 and (name NB or name ND or name C1A or na \ me C1B or name C1C or name C1D or name C2A or name C2B or name C2C or name C2D o \ r name C3A or name C3B or name C3C or name C3D or name C4A or name C4B or name C \ 4C or name C4D or name CAB or name CAC or name CAD or name CBB or name CBD or na \ me CED or name CGD or name CHA or name CHB or name CHC or name CHD or name CMA o \ r name CMB or name CMC or name CMD or name NA or name NC or name O1D or name O2D \ or name OBD or name MG )) or resid 611 through 613 or (resid 614 and (name NB o \ r name ND or name C1A or name C1B or name C1C or name C1D or name C2A or name C2 \ B or name C2C or name C2D or name C3A or name C3B or name C3C or name C3D or nam \ e C4A or name C4B or name C4C or name C4D or name CAA or name CAB or name CAC or \ name CAD or name CBD or name CGD or name CHA or name CHB or name CHC or name CH \ D or name CMB or name CMC or name CMD or name NA or name NC or name O1D or name \ O2D or name OBD or name MG )) or (resid 616 and (name NB or name ND or name C1A \ or name C1B or name C1C or name C1D or name C2A or name C2B or name C2C or name \ C2D or name C3A or name C3B or name C3C or name C3D or name C4A or name C4B or n \ ame C4C or name C4D or name CAA or name CAB or name CAC or name CAD or name CBA \ or name CBD or name CED or name CGA or name CGD or name CHA or name CHB or name \ CHC or name CHD or name CMA or name CMB or name CMC or name CMD or name NA or na \ me NC or name O1A or name O1D or name O2A or name O2D or name OBD or name MG )) \ or resid 617 through 620)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 4.870 Check model and map are aligned: 0.750 Set scattering table: 0.430 Process input model: 115.640 Find NCS groups from input model: 1.550 Set up NCS constraints: 0.170 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 137.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.020 1.429 47709 Z= 1.047 Angle : 2.043 40.678 68194 Z= 0.801 Chirality : 0.254 5.662 5602 Planarity : 0.011 0.305 8996 Dihedral : 22.328 126.181 15151 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.54 % Favored : 93.33 % Rotamer: Outliers : 0.42 % Allowed : 4.05 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.11), residues: 3851 helix: -2.59 (0.08), residues: 2104 sheet: -1.86 (0.54), residues: 72 loop : -2.39 (0.13), residues: 1675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.004 TRP A 612 HIS 0.026 0.003 HIS A 539 PHE 0.044 0.004 PHE A 360 TYR 0.052 0.004 TYR 3 89 ARG 0.017 0.002 ARG 3 96 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 848 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 835 time to evaluate : 3.705 Fit side-chains revert: symmetry clash REVERT: A 460 ASP cc_start: 0.8110 (m-30) cc_final: 0.7893 (m-30) REVERT: B 291 MET cc_start: 0.7035 (ttt) cc_final: 0.6797 (ttp) REVERT: B 411 ARG cc_start: 0.7287 (mmt180) cc_final: 0.7055 (mmm160) REVERT: B 476 ASP cc_start: 0.6015 (p0) cc_final: 0.5810 (m-30) REVERT: B 489 ASN cc_start: 0.6562 (m110) cc_final: 0.6237 (t0) REVERT: C 28 MET cc_start: 0.8508 (mmm) cc_final: 0.8264 (tpt) REVERT: C 37 SER cc_start: 0.8476 (m) cc_final: 0.8256 (t) REVERT: L 181 LEU cc_start: 0.7324 (tt) cc_final: 0.6864 (mt) REVERT: 1 63 SER cc_start: 0.7065 (t) cc_final: 0.6801 (p) REVERT: a 74 PRO cc_start: 0.8072 (Cg_endo) cc_final: 0.7781 (Cg_exo) REVERT: 3 124 LYS cc_start: 0.8352 (mtmm) cc_final: 0.8080 (mttt) REVERT: 3 255 ASN cc_start: 0.7784 (m110) cc_final: 0.7536 (m-40) REVERT: 4 179 GLN cc_start: 0.8970 (tt0) cc_final: 0.8738 (tt0) REVERT: 4 188 ILE cc_start: 0.9231 (mm) cc_final: 0.8878 (mt) REVERT: 4 279 SER cc_start: 0.8038 (m) cc_final: 0.7758 (p) REVERT: 5 133 ILE cc_start: 0.8317 (tp) cc_final: 0.8058 (tt) REVERT: 5 170 LYS cc_start: 0.8210 (mmtp) cc_final: 0.7953 (tmtp) REVERT: 7 46 SER cc_start: 0.8026 (p) cc_final: 0.7816 (m) REVERT: 7 123 ILE cc_start: 0.9057 (mt) cc_final: 0.8806 (mt) REVERT: 7 156 GLU cc_start: 0.7613 (mp0) cc_final: 0.7393 (mp0) REVERT: 8 110 MET cc_start: 0.9084 (mtm) cc_final: 0.8508 (mtm) REVERT: 8 169 ASP cc_start: 0.7859 (t70) cc_final: 0.7488 (t0) REVERT: 8 171 ARG cc_start: 0.7160 (mtp180) cc_final: 0.6879 (ptm160) REVERT: 8 264 THR cc_start: 0.8020 (m) cc_final: 0.7697 (p) outliers start: 13 outliers final: 8 residues processed: 840 average time/residue: 1.4158 time to fit residues: 1494.1594 Evaluate side-chains 471 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 463 time to evaluate : 3.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 202 HIS Chi-restraints excluded: chain 3 residue 138 ASN Chi-restraints excluded: chain 3 residue 218 ILE Chi-restraints excluded: chain 3 residue 261 ASN Chi-restraints excluded: chain 6 residue 311 CYS Chi-restraints excluded: chain 8 residue 267 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 5.9990 chunk 291 optimal weight: 20.0000 chunk 161 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 196 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 300 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 224 optimal weight: 20.0000 chunk 348 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 HIS A 268 ASN A 496 GLN A 609 HIS ** A 714 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN B 403 GLN ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 506 GLN D 130 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN F 127 ASN F 198 GLN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 232 ASN 1 237 ASN a 58 ASN a 76 ASN 3 94 HIS 3 175 GLN ** 3 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 209 ASN 5 176 ASN ** 5 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 191 GLN ** 6 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 63 GLN 7 70 GLN 7 124 GLN 8 105 HIS 8 129 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 47709 Z= 0.366 Angle : 1.072 28.083 68194 Z= 0.419 Chirality : 0.062 1.822 5602 Planarity : 0.007 0.060 8996 Dihedral : 23.304 113.855 8545 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 16.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 4.61 % Allowed : 12.55 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.12), residues: 3851 helix: -1.01 (0.10), residues: 2095 sheet: -1.70 (0.51), residues: 77 loop : -1.71 (0.15), residues: 1679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 425 HIS 0.016 0.002 HIS 6 135 PHE 0.026 0.002 PHE 4 169 TYR 0.025 0.002 TYR D 208 ARG 0.011 0.001 ARG 3 162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 480 time to evaluate : 3.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8866 (mmp) cc_final: 0.8612 (mmp) REVERT: A 324 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7022 (mp0) REVERT: B 175 ARG cc_start: 0.8404 (ttp80) cc_final: 0.8153 (ttp80) REVERT: B 206 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7852 (pt0) REVERT: B 411 ARG cc_start: 0.7676 (mmt180) cc_final: 0.7439 (mmt180) REVERT: C 35 LYS cc_start: 0.8211 (mmmm) cc_final: 0.7910 (mmtp) REVERT: C 37 SER cc_start: 0.8697 (m) cc_final: 0.8442 (t) REVERT: D 135 TYR cc_start: 0.8835 (m-80) cc_final: 0.8411 (m-80) REVERT: D 178 GLN cc_start: 0.8844 (OUTLIER) cc_final: 0.8563 (tt0) REVERT: E 95 GLU cc_start: 0.7643 (pt0) cc_final: 0.7360 (pt0) REVERT: F 195 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8669 (mm) REVERT: F 217 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7192 (tt0) REVERT: L 181 LEU cc_start: 0.7359 (tt) cc_final: 0.6865 (mt) REVERT: 1 63 SER cc_start: 0.7309 (t) cc_final: 0.6966 (p) REVERT: a 74 PRO cc_start: 0.8137 (Cg_endo) cc_final: 0.7879 (Cg_exo) REVERT: a 232 ASN cc_start: 0.7504 (t0) cc_final: 0.6666 (p0) REVERT: 3 205 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8224 (mttp) REVERT: 4 179 GLN cc_start: 0.8983 (tt0) cc_final: 0.8733 (tt0) REVERT: 7 46 SER cc_start: 0.8203 (p) cc_final: 0.7997 (m) REVERT: 7 101 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7825 (mm-30) REVERT: 7 123 ILE cc_start: 0.9143 (mt) cc_final: 0.8889 (mt) REVERT: 8 110 MET cc_start: 0.9118 (mtm) cc_final: 0.8490 (mtm) REVERT: 8 169 ASP cc_start: 0.7913 (t70) cc_final: 0.7665 (t0) REVERT: 8 171 ARG cc_start: 0.7227 (mtp180) cc_final: 0.7018 (ptm160) REVERT: 8 203 ASP cc_start: 0.7981 (t70) cc_final: 0.7711 (t0) REVERT: 8 264 THR cc_start: 0.8160 (m) cc_final: 0.7852 (p) outliers start: 141 outliers final: 59 residues processed: 567 average time/residue: 1.3392 time to fit residues: 974.1781 Evaluate side-chains 488 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 423 time to evaluate : 3.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 513 ASP Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 158 ARG Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 178 GLN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain 1 residue 106 MET Chi-restraints excluded: chain a residue 95 THR Chi-restraints excluded: chain a residue 113 LEU Chi-restraints excluded: chain 3 residue 138 ASN Chi-restraints excluded: chain 3 residue 205 LYS Chi-restraints excluded: chain 3 residue 218 ILE Chi-restraints excluded: chain 3 residue 240 LYS Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 4 residue 84 LEU Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 5 residue 115 VAL Chi-restraints excluded: chain 5 residue 131 THR Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 218 ILE Chi-restraints excluded: chain 5 residue 237 SER Chi-restraints excluded: chain 5 residue 250 THR Chi-restraints excluded: chain 5 residue 259 VAL Chi-restraints excluded: chain 5 residue 267 THR Chi-restraints excluded: chain 6 residue 192 ASP Chi-restraints excluded: chain 6 residue 230 LEU Chi-restraints excluded: chain 6 residue 258 THR Chi-restraints excluded: chain 6 residue 270 LEU Chi-restraints excluded: chain 6 residue 290 VAL Chi-restraints excluded: chain 7 residue 158 LYS Chi-restraints excluded: chain 7 residue 176 SER Chi-restraints excluded: chain 7 residue 196 LEU Chi-restraints excluded: chain 8 residue 93 VAL Chi-restraints excluded: chain 8 residue 248 ASP Chi-restraints excluded: chain 8 residue 254 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 193 optimal weight: 20.0000 chunk 108 optimal weight: 10.0000 chunk 290 optimal weight: 20.0000 chunk 237 optimal weight: 20.0000 chunk 96 optimal weight: 8.9990 chunk 349 optimal weight: 20.0000 chunk 377 optimal weight: 7.9990 chunk 311 optimal weight: 8.9990 chunk 346 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 280 optimal weight: 9.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 246 ASN A 496 GLN ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 403 GLN ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 628 ASN D 130 GLN ** E 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 ASN F 127 ASN F 198 GLN 1 214 GLN ** 3 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 155 GLN ** 5 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 124 GLN 7 230 ASN 8 100 GLN 8 129 ASN 8 155 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 47709 Z= 0.436 Angle : 1.065 26.356 68194 Z= 0.418 Chirality : 0.062 1.721 5602 Planarity : 0.007 0.059 8996 Dihedral : 21.860 114.640 8539 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 5.33 % Allowed : 13.53 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.13), residues: 3851 helix: -0.48 (0.11), residues: 2108 sheet: -1.30 (0.54), residues: 78 loop : -1.50 (0.15), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 583 HIS 0.015 0.002 HIS B 415 PHE 0.029 0.002 PHE 5 186 TYR 0.026 0.002 TYR 3 89 ARG 0.008 0.001 ARG 3 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 439 time to evaluate : 3.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 324 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: A 497 LEU cc_start: 0.8556 (pp) cc_final: 0.8261 (tt) REVERT: B 175 ARG cc_start: 0.8481 (ttp80) cc_final: 0.8165 (ttp80) REVERT: B 200 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8658 (mm) REVERT: B 206 GLN cc_start: 0.8283 (OUTLIER) cc_final: 0.7957 (pt0) REVERT: C 10 THR cc_start: 0.9350 (OUTLIER) cc_final: 0.9095 (p) REVERT: D 135 TYR cc_start: 0.8952 (m-80) cc_final: 0.8553 (m-80) REVERT: E 95 GLU cc_start: 0.7774 (pt0) cc_final: 0.7541 (pt0) REVERT: E 136 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7767 (mm) REVERT: F 63 ASP cc_start: 0.7123 (t70) cc_final: 0.6836 (t70) REVERT: F 108 MET cc_start: 0.7022 (mtt) cc_final: 0.6742 (mtt) REVERT: F 195 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8745 (mm) REVERT: F 217 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7204 (tt0) REVERT: I 101 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7409 (mmtt) REVERT: K 85 MET cc_start: 0.8523 (mmm) cc_final: 0.8319 (mmm) REVERT: L 181 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6869 (mt) REVERT: a 74 PRO cc_start: 0.8107 (Cg_endo) cc_final: 0.7857 (Cg_exo) REVERT: a 162 GLU cc_start: 0.8508 (mm-30) cc_final: 0.7591 (mm-30) REVERT: a 232 ASN cc_start: 0.7592 (t0) cc_final: 0.6804 (p0) REVERT: 3 205 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8356 (mttp) REVERT: 3 256 ASN cc_start: 0.8027 (t0) cc_final: 0.7812 (t0) REVERT: 4 120 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8139 (ptmt) REVERT: 4 167 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7054 (pp20) REVERT: 4 179 GLN cc_start: 0.9080 (tt0) cc_final: 0.8818 (tt0) REVERT: 4 279 SER cc_start: 0.8356 (OUTLIER) cc_final: 0.7976 (p) REVERT: 5 80 ASP cc_start: 0.7716 (t0) cc_final: 0.7499 (t0) REVERT: 6 123 GLU cc_start: 0.7677 (tt0) cc_final: 0.7447 (tm-30) REVERT: 6 149 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7616 (tt0) REVERT: 7 46 SER cc_start: 0.8374 (p) cc_final: 0.8082 (m) REVERT: 7 65 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9311 (tp) REVERT: 7 88 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8674 (tm) REVERT: 7 123 ILE cc_start: 0.9217 (mt) cc_final: 0.8967 (mt) REVERT: 8 110 MET cc_start: 0.9107 (mtm) cc_final: 0.8460 (mtm) REVERT: 8 203 ASP cc_start: 0.8170 (t70) cc_final: 0.7881 (t0) outliers start: 163 outliers final: 71 residues processed: 545 average time/residue: 1.3163 time to fit residues: 924.1658 Evaluate side-chains 495 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 409 time to evaluate : 3.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 101 LYS Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain K residue 133 ILE Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 193 CYS Chi-restraints excluded: chain 1 residue 101 HIS Chi-restraints excluded: chain 1 residue 171 VAL Chi-restraints excluded: chain 1 residue 243 ILE Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 131 VAL Chi-restraints excluded: chain a residue 171 VAL Chi-restraints excluded: chain a residue 226 LEU Chi-restraints excluded: chain 3 residue 138 ASN Chi-restraints excluded: chain 3 residue 205 LYS Chi-restraints excluded: chain 3 residue 218 ILE Chi-restraints excluded: chain 3 residue 240 LYS Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 3 residue 261 ASN Chi-restraints excluded: chain 4 residue 84 LEU Chi-restraints excluded: chain 4 residue 120 LYS Chi-restraints excluded: chain 4 residue 167 GLU Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 4 residue 271 SER Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 4 residue 286 ASP Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 5 residue 115 VAL Chi-restraints excluded: chain 5 residue 124 GLN Chi-restraints excluded: chain 5 residue 131 THR Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 237 SER Chi-restraints excluded: chain 5 residue 250 THR Chi-restraints excluded: chain 5 residue 259 VAL Chi-restraints excluded: chain 6 residue 230 LEU Chi-restraints excluded: chain 6 residue 258 THR Chi-restraints excluded: chain 6 residue 270 LEU Chi-restraints excluded: chain 6 residue 290 VAL Chi-restraints excluded: chain 6 residue 311 CYS Chi-restraints excluded: chain 7 residue 65 LEU Chi-restraints excluded: chain 7 residue 88 LEU Chi-restraints excluded: chain 7 residue 158 LYS Chi-restraints excluded: chain 7 residue 176 SER Chi-restraints excluded: chain 7 residue 196 LEU Chi-restraints excluded: chain 7 residue 229 VAL Chi-restraints excluded: chain 8 residue 58 SER Chi-restraints excluded: chain 8 residue 93 VAL Chi-restraints excluded: chain 8 residue 142 GLU Chi-restraints excluded: chain 8 residue 248 ASP Chi-restraints excluded: chain 8 residue 254 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 345 optimal weight: 3.9990 chunk 262 optimal weight: 5.9990 chunk 181 optimal weight: 8.9990 chunk 38 optimal weight: 0.9980 chunk 166 optimal weight: 4.9990 chunk 234 optimal weight: 6.9990 chunk 350 optimal weight: 9.9990 chunk 371 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 332 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 101 GLN F 117 ASN F 127 ASN F 198 GLN ** 3 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 155 GLN ** 5 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 222 GLN 6 256 GLN 7 124 GLN 8 129 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 47709 Z= 0.252 Angle : 0.959 26.327 68194 Z= 0.371 Chirality : 0.057 1.729 5602 Planarity : 0.005 0.057 8996 Dihedral : 20.880 109.233 8539 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.45 % Allowed : 15.33 % Favored : 80.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.13), residues: 3851 helix: -0.02 (0.11), residues: 2104 sheet: -1.00 (0.56), residues: 76 loop : -1.30 (0.15), residues: 1671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP a 129 HIS 0.010 0.002 HIS A 433 PHE 0.032 0.002 PHE B 487 TYR 0.024 0.002 TYR B 658 ARG 0.005 0.001 ARG 3 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 431 time to evaluate : 3.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 MET cc_start: 0.8841 (mmp) cc_final: 0.8532 (mmp) REVERT: A 324 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7023 (mp0) REVERT: A 415 ARG cc_start: 0.8686 (OUTLIER) cc_final: 0.8243 (mtm180) REVERT: A 497 LEU cc_start: 0.8440 (pp) cc_final: 0.8173 (tt) REVERT: A 676 HIS cc_start: 0.8960 (OUTLIER) cc_final: 0.8499 (m90) REVERT: B 175 ARG cc_start: 0.8171 (ttp80) cc_final: 0.7814 (ttp80) REVERT: B 200 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8596 (mm) REVERT: B 206 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7917 (pt0) REVERT: B 302 MET cc_start: 0.6404 (mtp) cc_final: 0.6110 (mmt) REVERT: B 411 ARG cc_start: 0.8149 (mtt180) cc_final: 0.7835 (mtp180) REVERT: C 10 THR cc_start: 0.9329 (OUTLIER) cc_final: 0.9088 (p) REVERT: C 24 ASP cc_start: 0.7667 (t0) cc_final: 0.7395 (t0) REVERT: D 135 TYR cc_start: 0.8899 (m-80) cc_final: 0.8576 (m-80) REVERT: D 148 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8429 (tt0) REVERT: E 95 GLU cc_start: 0.7713 (pt0) cc_final: 0.7381 (pt0) REVERT: E 136 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7802 (mm) REVERT: F 63 ASP cc_start: 0.6997 (t70) cc_final: 0.6750 (t70) REVERT: F 195 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8785 (mm) REVERT: F 217 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7296 (tt0) REVERT: K 85 MET cc_start: 0.8427 (mmm) cc_final: 0.8045 (mmm) REVERT: L 181 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6682 (mt) REVERT: a 101 HIS cc_start: 0.8236 (OUTLIER) cc_final: 0.7752 (m90) REVERT: a 162 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7758 (mm-30) REVERT: a 232 ASN cc_start: 0.7574 (t0) cc_final: 0.6862 (p0) REVERT: 3 205 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8263 (mttp) REVERT: 4 167 GLU cc_start: 0.7317 (OUTLIER) cc_final: 0.7050 (pp20) REVERT: 4 179 GLN cc_start: 0.9055 (tt0) cc_final: 0.8700 (tt0) REVERT: 5 80 ASP cc_start: 0.7491 (t0) cc_final: 0.7150 (t0) REVERT: 5 179 MET cc_start: 0.8479 (ttm) cc_final: 0.8234 (ttm) REVERT: 6 123 GLU cc_start: 0.7664 (tt0) cc_final: 0.7430 (tm-30) REVERT: 7 46 SER cc_start: 0.8311 (p) cc_final: 0.8096 (m) REVERT: 7 65 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9300 (tp) REVERT: 7 88 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8667 (tm) REVERT: 7 123 ILE cc_start: 0.9213 (mt) cc_final: 0.8994 (mt) REVERT: 7 156 GLU cc_start: 0.7749 (mp0) cc_final: 0.7449 (mp0) REVERT: 8 110 MET cc_start: 0.9055 (mtm) cc_final: 0.8365 (mtm) REVERT: 8 203 ASP cc_start: 0.8213 (t70) cc_final: 0.7931 (t0) REVERT: 8 208 SER cc_start: 0.8766 (m) cc_final: 0.8319 (t) outliers start: 136 outliers final: 68 residues processed: 529 average time/residue: 1.3069 time to fit residues: 889.7007 Evaluate side-chains 480 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 396 time to evaluate : 4.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 148 GLU Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 85 LYS Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 195 LEU Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 193 CYS Chi-restraints excluded: chain 1 residue 101 HIS Chi-restraints excluded: chain 1 residue 243 ILE Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 101 HIS Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain a residue 226 LEU Chi-restraints excluded: chain 3 residue 47 VAL Chi-restraints excluded: chain 3 residue 138 ASN Chi-restraints excluded: chain 3 residue 205 LYS Chi-restraints excluded: chain 3 residue 218 ILE Chi-restraints excluded: chain 3 residue 240 LYS Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 3 residue 261 ASN Chi-restraints excluded: chain 4 residue 84 LEU Chi-restraints excluded: chain 4 residue 167 GLU Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 5 residue 82 THR Chi-restraints excluded: chain 5 residue 115 VAL Chi-restraints excluded: chain 5 residue 124 GLN Chi-restraints excluded: chain 5 residue 131 THR Chi-restraints excluded: chain 5 residue 139 LEU Chi-restraints excluded: chain 5 residue 237 SER Chi-restraints excluded: chain 5 residue 259 VAL Chi-restraints excluded: chain 5 residue 267 THR Chi-restraints excluded: chain 6 residue 192 ASP Chi-restraints excluded: chain 6 residue 230 LEU Chi-restraints excluded: chain 6 residue 270 LEU Chi-restraints excluded: chain 6 residue 290 VAL Chi-restraints excluded: chain 6 residue 311 CYS Chi-restraints excluded: chain 7 residue 65 LEU Chi-restraints excluded: chain 7 residue 88 LEU Chi-restraints excluded: chain 7 residue 108 VAL Chi-restraints excluded: chain 7 residue 158 LYS Chi-restraints excluded: chain 7 residue 196 LEU Chi-restraints excluded: chain 7 residue 229 VAL Chi-restraints excluded: chain 8 residue 93 VAL Chi-restraints excluded: chain 8 residue 142 GLU Chi-restraints excluded: chain 8 residue 248 ASP Chi-restraints excluded: chain 8 residue 254 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 309 optimal weight: 0.2980 chunk 210 optimal weight: 4.9990 chunk 5 optimal weight: 9.9990 chunk 276 optimal weight: 10.0000 chunk 153 optimal weight: 1.9990 chunk 316 optimal weight: 4.9990 chunk 256 optimal weight: 0.0020 chunk 0 optimal weight: 0.7980 chunk 189 optimal weight: 5.9990 chunk 333 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 overall best weight: 1.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 HIS ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 101 GLN F 117 ASN F 127 ASN F 198 GLN 1 164 GLN ** 3 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 89 GLN 5 220 GLN ** 6 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 124 GLN 8 57 GLN 8 129 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 47709 Z= 0.161 Angle : 0.905 26.028 68194 Z= 0.346 Chirality : 0.054 1.719 5602 Planarity : 0.005 0.055 8996 Dihedral : 19.743 107.280 8539 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 3.99 % Allowed : 16.28 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.13), residues: 3851 helix: 0.39 (0.11), residues: 2100 sheet: -1.00 (0.55), residues: 73 loop : -1.12 (0.16), residues: 1678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP 8 148 HIS 0.007 0.001 HIS A 433 PHE 0.026 0.001 PHE 5 186 TYR 0.024 0.002 TYR B 658 ARG 0.006 0.000 ARG a 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 436 time to evaluate : 3.730 Fit side-chains REVERT: A 91 MET cc_start: 0.8824 (mmp) cc_final: 0.8559 (mmp) REVERT: A 497 LEU cc_start: 0.8394 (pp) cc_final: 0.8162 (tt) REVERT: A 584 CYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8435 (m) REVERT: A 676 HIS cc_start: 0.8830 (OUTLIER) cc_final: 0.8584 (m90) REVERT: B 175 ARG cc_start: 0.8244 (ttp80) cc_final: 0.7913 (ttp80) REVERT: B 206 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7883 (pt0) REVERT: B 411 ARG cc_start: 0.8001 (mtt180) cc_final: 0.7634 (mtp180) REVERT: B 609 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7443 (tm-30) REVERT: C 10 THR cc_start: 0.9284 (OUTLIER) cc_final: 0.9040 (p) REVERT: C 24 ASP cc_start: 0.7612 (t0) cc_final: 0.7354 (t0) REVERT: D 135 TYR cc_start: 0.8826 (m-80) cc_final: 0.8624 (m-80) REVERT: D 205 ASP cc_start: 0.8452 (p0) cc_final: 0.8084 (p0) REVERT: F 63 ASP cc_start: 0.6939 (t70) cc_final: 0.6688 (t70) REVERT: I 92 MET cc_start: 0.7495 (OUTLIER) cc_final: 0.6497 (mpp) REVERT: I 101 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7377 (mmtt) REVERT: K 85 MET cc_start: 0.8288 (mmm) cc_final: 0.7876 (mmm) REVERT: L 181 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6715 (mt) REVERT: a 101 HIS cc_start: 0.8169 (OUTLIER) cc_final: 0.7837 (m90) REVERT: a 162 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7680 (mm-30) REVERT: 4 167 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.7023 (pp20) REVERT: 5 80 ASP cc_start: 0.7367 (t0) cc_final: 0.7062 (t0) REVERT: 5 179 MET cc_start: 0.8408 (ttm) cc_final: 0.8153 (ttm) REVERT: 6 123 GLU cc_start: 0.7661 (tt0) cc_final: 0.7426 (tm-30) REVERT: 7 46 SER cc_start: 0.8270 (p) cc_final: 0.8040 (m) REVERT: 7 65 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9286 (tp) REVERT: 7 88 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8625 (tm) REVERT: 7 155 GLU cc_start: 0.6592 (pp20) cc_final: 0.6183 (pp20) REVERT: 8 110 MET cc_start: 0.9044 (mtm) cc_final: 0.8386 (mtm) REVERT: 8 186 GLU cc_start: 0.7706 (pm20) cc_final: 0.7493 (pm20) REVERT: 8 203 ASP cc_start: 0.8185 (t70) cc_final: 0.7897 (t0) REVERT: 8 208 SER cc_start: 0.8695 (m) cc_final: 0.8245 (t) REVERT: 8 212 ASP cc_start: 0.7598 (t0) cc_final: 0.7164 (p0) outliers start: 122 outliers final: 50 residues processed: 523 average time/residue: 1.3285 time to fit residues: 897.3604 Evaluate side-chains 467 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 405 time to evaluate : 3.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 176 LEU Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain I residue 92 MET Chi-restraints excluded: chain I residue 101 LYS Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 193 CYS Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 101 HIS Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain a residue 226 LEU Chi-restraints excluded: chain 3 residue 218 ILE Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 3 residue 261 ASN Chi-restraints excluded: chain 4 residue 84 LEU Chi-restraints excluded: chain 4 residue 167 GLU Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 4 residue 285 ASN Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 5 residue 115 VAL Chi-restraints excluded: chain 5 residue 131 THR Chi-restraints excluded: chain 5 residue 237 SER Chi-restraints excluded: chain 5 residue 252 THR Chi-restraints excluded: chain 5 residue 259 VAL Chi-restraints excluded: chain 6 residue 230 LEU Chi-restraints excluded: chain 6 residue 270 LEU Chi-restraints excluded: chain 6 residue 290 VAL Chi-restraints excluded: chain 6 residue 311 CYS Chi-restraints excluded: chain 7 residue 65 LEU Chi-restraints excluded: chain 7 residue 88 LEU Chi-restraints excluded: chain 7 residue 109 VAL Chi-restraints excluded: chain 8 residue 58 SER Chi-restraints excluded: chain 8 residue 93 VAL Chi-restraints excluded: chain 8 residue 142 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 124 optimal weight: 10.0000 chunk 334 optimal weight: 10.0000 chunk 73 optimal weight: 8.9990 chunk 217 optimal weight: 10.0000 chunk 91 optimal weight: 30.0000 chunk 371 optimal weight: 7.9990 chunk 308 optimal weight: 7.9990 chunk 172 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 195 optimal weight: 3.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN A 350 HIS ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN F 117 ASN F 127 ASN F 198 GLN K 119 ASN a 76 ASN a 232 ASN 3 245 ASN ** 4 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 164 ASN 5 222 GLN 6 191 GLN 6 256 GLN 7 124 GLN 8 129 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 47709 Z= 0.395 Angle : 1.004 26.194 68194 Z= 0.392 Chirality : 0.060 1.707 5602 Planarity : 0.006 0.057 8996 Dihedral : 19.820 111.926 8535 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 4.41 % Allowed : 16.84 % Favored : 78.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.13), residues: 3851 helix: 0.29 (0.11), residues: 2113 sheet: -1.12 (0.54), residues: 80 loop : -1.14 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 1 104 HIS 0.013 0.002 HIS B 415 PHE 0.035 0.002 PHE 5 186 TYR 0.030 0.002 TYR 1 77 ARG 0.007 0.001 ARG 3 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 405 time to evaluate : 3.993 Fit side-chains revert: symmetry clash REVERT: A 91 MET cc_start: 0.8896 (mmp) cc_final: 0.8691 (mmp) REVERT: A 415 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8367 (mtm180) REVERT: A 497 LEU cc_start: 0.8452 (pp) cc_final: 0.8189 (tt) REVERT: A 676 HIS cc_start: 0.9028 (OUTLIER) cc_final: 0.8459 (m90) REVERT: B 107 ARG cc_start: 0.7446 (OUTLIER) cc_final: 0.6967 (pmt170) REVERT: B 206 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7929 (pt0) REVERT: B 411 ARG cc_start: 0.7984 (mtt180) cc_final: 0.7736 (mtp180) REVERT: C 10 THR cc_start: 0.9337 (OUTLIER) cc_final: 0.9076 (p) REVERT: C 24 ASP cc_start: 0.7639 (t0) cc_final: 0.7372 (t0) REVERT: E 136 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7771 (mm) REVERT: F 63 ASP cc_start: 0.7031 (t70) cc_final: 0.6780 (t70) REVERT: F 217 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7053 (tt0) REVERT: I 101 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7307 (mmtt) REVERT: K 85 MET cc_start: 0.8321 (mmm) cc_final: 0.7823 (mmm) REVERT: L 181 LEU cc_start: 0.7151 (OUTLIER) cc_final: 0.6659 (mt) REVERT: 1 58 ASN cc_start: 0.8344 (t0) cc_final: 0.8118 (t0) REVERT: a 101 HIS cc_start: 0.8276 (OUTLIER) cc_final: 0.7701 (m90) REVERT: a 113 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7282 (pp) REVERT: a 162 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7948 (mm-30) REVERT: a 232 ASN cc_start: 0.7600 (t0) cc_final: 0.6889 (p0) REVERT: 3 205 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8097 (mttp) REVERT: 4 167 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6996 (pp20) REVERT: 6 123 GLU cc_start: 0.7687 (tt0) cc_final: 0.7436 (tm-30) REVERT: 6 201 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.7802 (tm-30) REVERT: 7 46 SER cc_start: 0.8498 (p) cc_final: 0.8162 (m) REVERT: 7 65 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.9300 (tp) REVERT: 7 88 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8642 (tm) REVERT: 8 110 MET cc_start: 0.9102 (mtm) cc_final: 0.8451 (mtm) REVERT: 8 203 ASP cc_start: 0.8217 (t70) cc_final: 0.7927 (t0) REVERT: 8 208 SER cc_start: 0.8804 (m) cc_final: 0.8442 (t) outliers start: 135 outliers final: 75 residues processed: 504 average time/residue: 1.3827 time to fit residues: 897.9997 Evaluate side-chains 483 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 392 time to evaluate : 4.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 136 LEU Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 101 LYS Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 193 CYS Chi-restraints excluded: chain 1 residue 92 LYS Chi-restraints excluded: chain 1 residue 101 HIS Chi-restraints excluded: chain 1 residue 172 VAL Chi-restraints excluded: chain 1 residue 243 ILE Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 98 GLU Chi-restraints excluded: chain a residue 101 HIS Chi-restraints excluded: chain a residue 113 LEU Chi-restraints excluded: chain a residue 171 VAL Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain a residue 226 LEU Chi-restraints excluded: chain 3 residue 47 VAL Chi-restraints excluded: chain 3 residue 138 ASN Chi-restraints excluded: chain 3 residue 205 LYS Chi-restraints excluded: chain 3 residue 218 ILE Chi-restraints excluded: chain 3 residue 240 LYS Chi-restraints excluded: chain 3 residue 259 LEU Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 3 residue 261 ASN Chi-restraints excluded: chain 4 residue 84 LEU Chi-restraints excluded: chain 4 residue 148 ASN Chi-restraints excluded: chain 4 residue 167 GLU Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 4 residue 285 ASN Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 5 residue 82 THR Chi-restraints excluded: chain 5 residue 115 VAL Chi-restraints excluded: chain 5 residue 131 THR Chi-restraints excluded: chain 5 residue 237 SER Chi-restraints excluded: chain 5 residue 252 THR Chi-restraints excluded: chain 5 residue 259 VAL Chi-restraints excluded: chain 6 residue 201 GLN Chi-restraints excluded: chain 6 residue 230 LEU Chi-restraints excluded: chain 6 residue 270 LEU Chi-restraints excluded: chain 6 residue 290 VAL Chi-restraints excluded: chain 6 residue 311 CYS Chi-restraints excluded: chain 7 residue 65 LEU Chi-restraints excluded: chain 7 residue 88 LEU Chi-restraints excluded: chain 7 residue 109 VAL Chi-restraints excluded: chain 7 residue 158 LYS Chi-restraints excluded: chain 8 residue 58 SER Chi-restraints excluded: chain 8 residue 93 VAL Chi-restraints excluded: chain 8 residue 142 GLU Chi-restraints excluded: chain 8 residue 248 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 358 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 211 optimal weight: 50.0000 chunk 271 optimal weight: 6.9990 chunk 210 optimal weight: 20.0000 chunk 312 optimal weight: 10.0000 chunk 207 optimal weight: 40.0000 chunk 370 optimal weight: 10.0000 chunk 231 optimal weight: 8.9990 chunk 225 optimal weight: 10.0000 chunk 170 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN E 101 GLN F 117 ASN F 127 ASN F 198 GLN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 124 GLN 8 129 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 47709 Z= 0.332 Angle : 0.973 26.069 68194 Z= 0.379 Chirality : 0.058 1.708 5602 Planarity : 0.006 0.057 8996 Dihedral : 19.663 109.051 8533 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.22 % Allowed : 17.65 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.13), residues: 3851 helix: 0.34 (0.11), residues: 2110 sheet: -1.04 (0.54), residues: 79 loop : -1.06 (0.16), residues: 1662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP 8 148 HIS 0.012 0.002 HIS B 415 PHE 0.029 0.002 PHE a 153 TYR 0.024 0.002 TYR B 658 ARG 0.006 0.001 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 398 time to evaluate : 3.797 Fit side-chains revert: symmetry clash REVERT: A 91 MET cc_start: 0.8830 (mmp) cc_final: 0.8620 (mmp) REVERT: A 415 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8359 (mtm180) REVERT: A 497 LEU cc_start: 0.8427 (pp) cc_final: 0.8162 (tt) REVERT: A 676 HIS cc_start: 0.9020 (OUTLIER) cc_final: 0.8509 (m90) REVERT: B 107 ARG cc_start: 0.7429 (OUTLIER) cc_final: 0.6948 (pmt170) REVERT: B 206 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7935 (pt0) REVERT: B 411 ARG cc_start: 0.8011 (mtt180) cc_final: 0.7703 (mtp180) REVERT: B 489 ASN cc_start: 0.6902 (m110) cc_final: 0.6304 (t0) REVERT: B 609 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: C 10 THR cc_start: 0.9348 (OUTLIER) cc_final: 0.9097 (p) REVERT: C 24 ASP cc_start: 0.7678 (t0) cc_final: 0.7473 (t0) REVERT: F 63 ASP cc_start: 0.6899 (t70) cc_final: 0.6680 (t70) REVERT: F 108 MET cc_start: 0.6981 (mtt) cc_final: 0.6645 (mtt) REVERT: F 217 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7119 (tt0) REVERT: I 92 MET cc_start: 0.7626 (OUTLIER) cc_final: 0.6405 (mpp) REVERT: I 101 LYS cc_start: 0.7765 (OUTLIER) cc_final: 0.7372 (mmtt) REVERT: K 85 MET cc_start: 0.8320 (mmm) cc_final: 0.7798 (mmm) REVERT: L 181 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6666 (mt) REVERT: a 101 HIS cc_start: 0.8241 (OUTLIER) cc_final: 0.7676 (m90) REVERT: a 113 LEU cc_start: 0.7775 (OUTLIER) cc_final: 0.7387 (pp) REVERT: 3 205 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8104 (mttp) REVERT: 4 167 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.7009 (pp20) REVERT: 6 123 GLU cc_start: 0.7683 (tt0) cc_final: 0.7389 (tm-30) REVERT: 6 201 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7768 (tm-30) REVERT: 7 46 SER cc_start: 0.8507 (p) cc_final: 0.8156 (m) REVERT: 7 65 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9306 (tp) REVERT: 7 88 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8628 (tm) REVERT: 8 110 MET cc_start: 0.9095 (mtm) cc_final: 0.8439 (mtm) REVERT: 8 203 ASP cc_start: 0.8211 (t70) cc_final: 0.7934 (t0) REVERT: 8 208 SER cc_start: 0.8734 (m) cc_final: 0.8526 (t) REVERT: 8 212 ASP cc_start: 0.7754 (t0) cc_final: 0.7432 (p0) outliers start: 129 outliers final: 81 residues processed: 493 average time/residue: 1.3285 time to fit residues: 840.2868 Evaluate side-chains 483 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 385 time to evaluate : 4.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 512 THR Chi-restraints excluded: chain B residue 591 VAL Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 197 LYS Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain I residue 92 MET Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 101 LYS Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 193 CYS Chi-restraints excluded: chain 1 residue 101 HIS Chi-restraints excluded: chain 1 residue 243 ILE Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 101 HIS Chi-restraints excluded: chain a residue 113 LEU Chi-restraints excluded: chain a residue 171 VAL Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain a residue 226 LEU Chi-restraints excluded: chain 3 residue 47 VAL Chi-restraints excluded: chain 3 residue 138 ASN Chi-restraints excluded: chain 3 residue 205 LYS Chi-restraints excluded: chain 3 residue 218 ILE Chi-restraints excluded: chain 3 residue 259 LEU Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 3 residue 261 ASN Chi-restraints excluded: chain 4 residue 84 LEU Chi-restraints excluded: chain 4 residue 93 LEU Chi-restraints excluded: chain 4 residue 148 ASN Chi-restraints excluded: chain 4 residue 167 GLU Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 4 residue 285 ASN Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 5 residue 82 THR Chi-restraints excluded: chain 5 residue 115 VAL Chi-restraints excluded: chain 5 residue 124 GLN Chi-restraints excluded: chain 5 residue 131 THR Chi-restraints excluded: chain 5 residue 237 SER Chi-restraints excluded: chain 5 residue 252 THR Chi-restraints excluded: chain 5 residue 259 VAL Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 192 ASP Chi-restraints excluded: chain 6 residue 201 GLN Chi-restraints excluded: chain 6 residue 230 LEU Chi-restraints excluded: chain 6 residue 270 LEU Chi-restraints excluded: chain 6 residue 290 VAL Chi-restraints excluded: chain 6 residue 311 CYS Chi-restraints excluded: chain 7 residue 65 LEU Chi-restraints excluded: chain 7 residue 88 LEU Chi-restraints excluded: chain 7 residue 109 VAL Chi-restraints excluded: chain 7 residue 158 LYS Chi-restraints excluded: chain 8 residue 58 SER Chi-restraints excluded: chain 8 residue 93 VAL Chi-restraints excluded: chain 8 residue 142 GLU Chi-restraints excluded: chain 8 residue 248 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 228 optimal weight: 0.0870 chunk 147 optimal weight: 10.0000 chunk 221 optimal weight: 8.9990 chunk 111 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 252 optimal weight: 30.0000 chunk 182 optimal weight: 7.9990 chunk 34 optimal weight: 6.9990 chunk 290 optimal weight: 20.0000 overall best weight: 5.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN F 117 ASN F 127 ASN F 198 GLN ** K 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 232 ASN ** 4 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 222 GLN 7 124 GLN 8 129 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 47709 Z= 0.295 Angle : 0.961 25.959 68194 Z= 0.373 Chirality : 0.057 1.705 5602 Planarity : 0.006 0.058 8996 Dihedral : 19.495 108.468 8533 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 17.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.32 % Allowed : 17.75 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.14), residues: 3851 helix: 0.41 (0.11), residues: 2116 sheet: -0.95 (0.56), residues: 77 loop : -1.01 (0.16), residues: 1658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP 8 148 HIS 0.015 0.002 HIS B 415 PHE 0.038 0.002 PHE B 487 TYR 0.026 0.002 TYR 6 302 ARG 0.008 0.001 ARG B 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 533 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 401 time to evaluate : 3.810 Fit side-chains revert: symmetry clash REVERT: A 91 MET cc_start: 0.8851 (mmp) cc_final: 0.8636 (mmp) REVERT: A 156 GLU cc_start: 0.7501 (mt-10) cc_final: 0.7222 (mp0) REVERT: A 415 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8350 (mtm180) REVERT: A 497 LEU cc_start: 0.8393 (pp) cc_final: 0.8121 (tt) REVERT: A 676 HIS cc_start: 0.9001 (OUTLIER) cc_final: 0.8500 (m90) REVERT: B 107 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6934 (pmt170) REVERT: B 175 ARG cc_start: 0.8414 (ttp80) cc_final: 0.8131 (ttp80) REVERT: B 206 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7939 (pt0) REVERT: B 411 ARG cc_start: 0.8003 (mtt180) cc_final: 0.7753 (mtp180) REVERT: B 489 ASN cc_start: 0.6856 (m110) cc_final: 0.6256 (t0) REVERT: B 609 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8076 (tt0) REVERT: C 10 THR cc_start: 0.9343 (OUTLIER) cc_final: 0.9084 (p) REVERT: F 63 ASP cc_start: 0.6907 (t70) cc_final: 0.6670 (t70) REVERT: F 217 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7105 (tt0) REVERT: I 101 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7372 (mmtt) REVERT: K 85 MET cc_start: 0.8302 (mmm) cc_final: 0.7776 (mmm) REVERT: L 181 LEU cc_start: 0.7096 (OUTLIER) cc_final: 0.6650 (mt) REVERT: a 101 HIS cc_start: 0.8231 (OUTLIER) cc_final: 0.7596 (m90) REVERT: a 162 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7710 (mm-30) REVERT: 3 205 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7990 (mttp) REVERT: 4 167 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.7002 (pp20) REVERT: 6 123 GLU cc_start: 0.7686 (tt0) cc_final: 0.7383 (tm-30) REVERT: 6 201 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7755 (tm-30) REVERT: 6 268 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.6970 (mp0) REVERT: 7 46 SER cc_start: 0.8485 (p) cc_final: 0.8139 (m) REVERT: 7 65 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9303 (tp) REVERT: 7 88 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8597 (tm) REVERT: 8 110 MET cc_start: 0.9087 (mtm) cc_final: 0.8369 (mtm) REVERT: 8 157 PHE cc_start: 0.8022 (m-10) cc_final: 0.7820 (m-10) REVERT: 8 203 ASP cc_start: 0.8209 (t70) cc_final: 0.7927 (t0) REVERT: 8 212 ASP cc_start: 0.7772 (t0) cc_final: 0.7479 (p0) outliers start: 132 outliers final: 83 residues processed: 495 average time/residue: 1.3562 time to fit residues: 858.4424 Evaluate side-chains 488 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 389 time to evaluate : 4.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 233 ASP Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 212 VAL Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain F residue 217 GLU Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 101 LYS Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 14 ILE Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain L residue 141 VAL Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 193 CYS Chi-restraints excluded: chain 1 residue 92 LYS Chi-restraints excluded: chain 1 residue 101 HIS Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 172 VAL Chi-restraints excluded: chain 1 residue 243 ILE Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 98 GLU Chi-restraints excluded: chain a residue 101 HIS Chi-restraints excluded: chain a residue 171 VAL Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain a residue 226 LEU Chi-restraints excluded: chain 3 residue 47 VAL Chi-restraints excluded: chain 3 residue 138 ASN Chi-restraints excluded: chain 3 residue 152 ILE Chi-restraints excluded: chain 3 residue 205 LYS Chi-restraints excluded: chain 3 residue 218 ILE Chi-restraints excluded: chain 3 residue 259 LEU Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 3 residue 261 ASN Chi-restraints excluded: chain 4 residue 84 LEU Chi-restraints excluded: chain 4 residue 148 ASN Chi-restraints excluded: chain 4 residue 167 GLU Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 5 residue 57 VAL Chi-restraints excluded: chain 5 residue 82 THR Chi-restraints excluded: chain 5 residue 124 GLN Chi-restraints excluded: chain 5 residue 131 THR Chi-restraints excluded: chain 5 residue 237 SER Chi-restraints excluded: chain 5 residue 252 THR Chi-restraints excluded: chain 5 residue 259 VAL Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 201 GLN Chi-restraints excluded: chain 6 residue 230 LEU Chi-restraints excluded: chain 6 residue 268 GLU Chi-restraints excluded: chain 6 residue 270 LEU Chi-restraints excluded: chain 6 residue 290 VAL Chi-restraints excluded: chain 6 residue 311 CYS Chi-restraints excluded: chain 7 residue 65 LEU Chi-restraints excluded: chain 7 residue 88 LEU Chi-restraints excluded: chain 7 residue 109 VAL Chi-restraints excluded: chain 7 residue 158 LYS Chi-restraints excluded: chain 8 residue 58 SER Chi-restraints excluded: chain 8 residue 93 VAL Chi-restraints excluded: chain 8 residue 142 GLU Chi-restraints excluded: chain 8 residue 248 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 336 optimal weight: 9.9990 chunk 354 optimal weight: 5.9990 chunk 323 optimal weight: 10.0000 chunk 344 optimal weight: 0.9990 chunk 207 optimal weight: 50.0000 chunk 150 optimal weight: 7.9990 chunk 270 optimal weight: 8.9990 chunk 105 optimal weight: 50.0000 chunk 311 optimal weight: 8.9990 chunk 326 optimal weight: 2.9990 chunk 343 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN F 117 ASN F 127 ASN F 198 GLN a 232 ASN ** 4 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 269 ASN 7 124 GLN 8 129 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 47709 Z= 0.237 Angle : 0.932 25.800 68194 Z= 0.362 Chirality : 0.056 1.709 5602 Planarity : 0.005 0.058 8996 Dihedral : 19.187 107.459 8533 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 17.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 3.60 % Allowed : 18.96 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.14), residues: 3851 helix: 0.53 (0.11), residues: 2111 sheet: -0.94 (0.56), residues: 77 loop : -0.96 (0.16), residues: 1663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP 8 148 HIS 0.014 0.001 HIS B 415 PHE 0.038 0.002 PHE 5 186 TYR 0.025 0.002 TYR B 658 ARG 0.007 0.001 ARG B 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 404 time to evaluate : 3.929 Fit side-chains revert: symmetry clash REVERT: A 156 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7201 (mp0) REVERT: A 415 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8336 (mtm180) REVERT: A 497 LEU cc_start: 0.8402 (pp) cc_final: 0.8156 (tt) REVERT: A 676 HIS cc_start: 0.8944 (OUTLIER) cc_final: 0.8573 (m90) REVERT: B 107 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6993 (pmt170) REVERT: B 206 GLN cc_start: 0.8197 (OUTLIER) cc_final: 0.7899 (pt0) REVERT: B 411 ARG cc_start: 0.7975 (mtt180) cc_final: 0.7744 (mtp180) REVERT: B 489 ASN cc_start: 0.7062 (m110) cc_final: 0.6416 (t0) REVERT: B 609 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8059 (tt0) REVERT: C 10 THR cc_start: 0.9325 (OUTLIER) cc_final: 0.9071 (p) REVERT: C 24 ASP cc_start: 0.7675 (t0) cc_final: 0.7459 (t0) REVERT: F 63 ASP cc_start: 0.6851 (t70) cc_final: 0.6631 (t70) REVERT: I 101 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7345 (mmtt) REVERT: K 85 MET cc_start: 0.8322 (mmm) cc_final: 0.7808 (mmm) REVERT: L 181 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6592 (mt) REVERT: a 101 HIS cc_start: 0.8228 (OUTLIER) cc_final: 0.7624 (m90) REVERT: a 162 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7658 (mm-30) REVERT: 4 167 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6971 (pp20) REVERT: 6 123 GLU cc_start: 0.7684 (tt0) cc_final: 0.7377 (tm-30) REVERT: 6 201 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7746 (tm-30) REVERT: 6 268 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7096 (mp0) REVERT: 7 46 SER cc_start: 0.8422 (p) cc_final: 0.8067 (m) REVERT: 7 88 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8585 (tm) REVERT: 7 155 GLU cc_start: 0.6778 (pp20) cc_final: 0.6481 (pp20) REVERT: 8 110 MET cc_start: 0.9075 (mtm) cc_final: 0.8388 (mtm) REVERT: 8 203 ASP cc_start: 0.8199 (t70) cc_final: 0.7934 (t0) REVERT: 8 212 ASP cc_start: 0.7689 (t0) cc_final: 0.7416 (p0) REVERT: 8 218 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8780 (mttt) outliers start: 110 outliers final: 70 residues processed: 482 average time/residue: 1.3084 time to fit residues: 814.0330 Evaluate side-chains 480 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 396 time to evaluate : 3.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 101 LYS Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain 1 residue 92 LYS Chi-restraints excluded: chain 1 residue 101 HIS Chi-restraints excluded: chain 1 residue 172 VAL Chi-restraints excluded: chain 1 residue 243 ILE Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 98 GLU Chi-restraints excluded: chain a residue 101 HIS Chi-restraints excluded: chain a residue 171 VAL Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain a residue 226 LEU Chi-restraints excluded: chain 3 residue 47 VAL Chi-restraints excluded: chain 3 residue 138 ASN Chi-restraints excluded: chain 3 residue 152 ILE Chi-restraints excluded: chain 3 residue 218 ILE Chi-restraints excluded: chain 3 residue 259 LEU Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 3 residue 261 ASN Chi-restraints excluded: chain 4 residue 84 LEU Chi-restraints excluded: chain 4 residue 167 GLU Chi-restraints excluded: chain 4 residue 201 ASN Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 5 residue 82 THR Chi-restraints excluded: chain 5 residue 131 THR Chi-restraints excluded: chain 5 residue 237 SER Chi-restraints excluded: chain 5 residue 252 THR Chi-restraints excluded: chain 5 residue 259 VAL Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 201 GLN Chi-restraints excluded: chain 6 residue 268 GLU Chi-restraints excluded: chain 6 residue 270 LEU Chi-restraints excluded: chain 6 residue 290 VAL Chi-restraints excluded: chain 6 residue 311 CYS Chi-restraints excluded: chain 7 residue 88 LEU Chi-restraints excluded: chain 7 residue 109 VAL Chi-restraints excluded: chain 7 residue 158 LYS Chi-restraints excluded: chain 8 residue 58 SER Chi-restraints excluded: chain 8 residue 93 VAL Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 218 LYS Chi-restraints excluded: chain 8 residue 248 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 226 optimal weight: 50.0000 chunk 364 optimal weight: 0.6980 chunk 222 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 253 optimal weight: 7.9990 chunk 382 optimal weight: 7.9990 chunk 352 optimal weight: 5.9990 chunk 304 optimal weight: 5.9990 chunk 31 optimal weight: 9.9990 chunk 235 optimal weight: 6.9990 chunk 186 optimal weight: 0.1980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN F 117 ASN F 127 ASN F 198 GLN 1 58 ASN a 232 ASN ** 3 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 222 GLN 7 124 GLN 8 129 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 47709 Z= 0.224 Angle : 0.923 25.719 68194 Z= 0.358 Chirality : 0.055 1.708 5602 Planarity : 0.005 0.091 8996 Dihedral : 18.937 107.589 8533 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.04 % Allowed : 19.81 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.14), residues: 3851 helix: 0.61 (0.11), residues: 2112 sheet: -1.00 (0.56), residues: 74 loop : -0.92 (0.16), residues: 1665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP a 129 HIS 0.014 0.001 HIS B 415 PHE 0.035 0.001 PHE B 487 TYR 0.027 0.002 TYR B 658 ARG 0.009 0.001 ARG B 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7702 Ramachandran restraints generated. 3851 Oldfield, 0 Emsley, 3851 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 407 time to evaluate : 3.597 Fit side-chains revert: symmetry clash REVERT: A 91 MET cc_start: 0.8743 (mmp) cc_final: 0.8365 (mmp) REVERT: A 156 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7189 (mp0) REVERT: A 415 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8330 (mtm180) REVERT: A 497 LEU cc_start: 0.8409 (pp) cc_final: 0.8190 (tt) REVERT: A 676 HIS cc_start: 0.8942 (OUTLIER) cc_final: 0.8574 (m90) REVERT: B 107 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.7000 (pmt170) REVERT: B 206 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7892 (pt0) REVERT: B 489 ASN cc_start: 0.6896 (m110) cc_final: 0.6344 (t0) REVERT: B 609 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8062 (tt0) REVERT: C 10 THR cc_start: 0.9310 (OUTLIER) cc_final: 0.9050 (p) REVERT: C 24 ASP cc_start: 0.7678 (t0) cc_final: 0.7474 (t0) REVERT: D 205 ASP cc_start: 0.8354 (p0) cc_final: 0.8020 (p0) REVERT: F 63 ASP cc_start: 0.6871 (t70) cc_final: 0.6646 (t70) REVERT: F 108 MET cc_start: 0.6802 (mtt) cc_final: 0.6474 (mtt) REVERT: I 92 MET cc_start: 0.7697 (tpp) cc_final: 0.7118 (mtt) REVERT: I 101 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7372 (mmtt) REVERT: K 85 MET cc_start: 0.8256 (mmm) cc_final: 0.7749 (mmm) REVERT: L 181 LEU cc_start: 0.7033 (OUTLIER) cc_final: 0.6583 (mt) REVERT: a 101 HIS cc_start: 0.8226 (OUTLIER) cc_final: 0.7617 (m90) REVERT: a 113 LEU cc_start: 0.7573 (mm) cc_final: 0.7220 (pp) REVERT: a 162 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7477 (mm-30) REVERT: 4 167 GLU cc_start: 0.7290 (OUTLIER) cc_final: 0.6964 (pp20) REVERT: 5 198 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7573 (tp30) REVERT: 6 123 GLU cc_start: 0.7684 (tt0) cc_final: 0.7377 (tm-30) REVERT: 6 201 GLN cc_start: 0.7961 (OUTLIER) cc_final: 0.7760 (tm-30) REVERT: 6 268 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.7140 (mp0) REVERT: 7 46 SER cc_start: 0.8448 (p) cc_final: 0.8118 (m) REVERT: 7 88 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8547 (tm) REVERT: 8 110 MET cc_start: 0.9071 (mtm) cc_final: 0.8386 (mtm) REVERT: 8 203 ASP cc_start: 0.8198 (t70) cc_final: 0.7939 (t0) REVERT: 8 212 ASP cc_start: 0.7662 (t0) cc_final: 0.7403 (p0) REVERT: 8 218 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8823 (mttt) outliers start: 93 outliers final: 71 residues processed: 471 average time/residue: 1.3273 time to fit residues: 806.0156 Evaluate side-chains 485 residues out of total 3060 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 400 time to evaluate : 3.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 293 ASP Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 415 ARG Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 584 CYS Chi-restraints excluded: chain A residue 592 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 676 HIS Chi-restraints excluded: chain A residue 701 VAL Chi-restraints excluded: chain A residue 709 VAL Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 107 ARG Chi-restraints excluded: chain B residue 140 SER Chi-restraints excluded: chain B residue 206 GLN Chi-restraints excluded: chain B residue 224 THR Chi-restraints excluded: chain B residue 290 HIS Chi-restraints excluded: chain B residue 368 THR Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 691 LEU Chi-restraints excluded: chain B residue 696 ASP Chi-restraints excluded: chain C residue 10 THR Chi-restraints excluded: chain C residue 32 ASP Chi-restraints excluded: chain C residue 37 SER Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 115 SER Chi-restraints excluded: chain D residue 173 LEU Chi-restraints excluded: chain D residue 217 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 137 ASP Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 128 ASP Chi-restraints excluded: chain F residue 174 VAL Chi-restraints excluded: chain I residue 95 LEU Chi-restraints excluded: chain I residue 101 LYS Chi-restraints excluded: chain J residue 8 LEU Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain J residue 35 ASP Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain 1 residue 101 HIS Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 172 VAL Chi-restraints excluded: chain 1 residue 243 ILE Chi-restraints excluded: chain a residue 91 LEU Chi-restraints excluded: chain a residue 98 GLU Chi-restraints excluded: chain a residue 101 HIS Chi-restraints excluded: chain a residue 171 VAL Chi-restraints excluded: chain a residue 206 VAL Chi-restraints excluded: chain a residue 226 LEU Chi-restraints excluded: chain 3 residue 47 VAL Chi-restraints excluded: chain 3 residue 138 ASN Chi-restraints excluded: chain 3 residue 152 ILE Chi-restraints excluded: chain 3 residue 218 ILE Chi-restraints excluded: chain 3 residue 259 LEU Chi-restraints excluded: chain 3 residue 260 THR Chi-restraints excluded: chain 4 residue 84 LEU Chi-restraints excluded: chain 4 residue 167 GLU Chi-restraints excluded: chain 4 residue 201 ASN Chi-restraints excluded: chain 4 residue 265 THR Chi-restraints excluded: chain 4 residue 279 SER Chi-restraints excluded: chain 5 residue 82 THR Chi-restraints excluded: chain 5 residue 124 GLN Chi-restraints excluded: chain 5 residue 131 THR Chi-restraints excluded: chain 5 residue 237 SER Chi-restraints excluded: chain 5 residue 252 THR Chi-restraints excluded: chain 5 residue 259 VAL Chi-restraints excluded: chain 6 residue 106 ASP Chi-restraints excluded: chain 6 residue 192 ASP Chi-restraints excluded: chain 6 residue 201 GLN Chi-restraints excluded: chain 6 residue 268 GLU Chi-restraints excluded: chain 6 residue 270 LEU Chi-restraints excluded: chain 6 residue 290 VAL Chi-restraints excluded: chain 6 residue 311 CYS Chi-restraints excluded: chain 7 residue 88 LEU Chi-restraints excluded: chain 7 residue 109 VAL Chi-restraints excluded: chain 7 residue 158 LYS Chi-restraints excluded: chain 8 residue 58 SER Chi-restraints excluded: chain 8 residue 93 VAL Chi-restraints excluded: chain 8 residue 117 LEU Chi-restraints excluded: chain 8 residue 218 LYS Chi-restraints excluded: chain 8 residue 248 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 241 optimal weight: 8.9990 chunk 324 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 280 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 305 optimal weight: 0.9990 chunk 127 optimal weight: 6.9990 chunk 313 optimal weight: 5.9990 chunk 38 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 445 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 GLN F 117 ASN F 127 ASN F 198 GLN a 58 ASN a 76 ASN a 232 ASN ** 3 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 202 GLN ** 4 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 124 GLN 8 129 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.122070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.092340 restraints weight = 74998.239| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.66 r_work: 0.2911 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 47709 Z= 0.270 Angle : 0.940 25.759 68194 Z= 0.367 Chirality : 0.056 1.708 5602 Planarity : 0.006 0.087 8996 Dihedral : 18.931 108.365 8533 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.24 % Allowed : 19.71 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3851 helix: 0.60 (0.11), residues: 2107 sheet: -1.01 (0.56), residues: 74 loop : -0.92 (0.16), residues: 1670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP a 129 HIS 0.014 0.002 HIS B 415 PHE 0.032 0.002 PHE 5 186 TYR 0.027 0.002 TYR B 658 ARG 0.017 0.001 ARG B 175 =============================================================================== Job complete usr+sys time: 14715.69 seconds wall clock time: 265 minutes 31.10 seconds (15931.10 seconds total)