Starting phenix.real_space_refine on Sun Mar 24 01:02:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uws_26841/03_2024/7uws_26841.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uws_26841/03_2024/7uws_26841.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uws_26841/03_2024/7uws_26841.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uws_26841/03_2024/7uws_26841.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uws_26841/03_2024/7uws_26841.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uws_26841/03_2024/7uws_26841.pdb" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 68 5.49 5 S 201 5.16 5 C 25140 2.51 5 N 6464 2.21 5 O 7543 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 33": "NH1" <-> "NH2" Residue "A ARG 81": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 179": "NH1" <-> "NH2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "A GLU 267": "OE1" <-> "OE2" Residue "A ARG 314": "NH1" <-> "NH2" Residue "A ARG 373": "NH1" <-> "NH2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "B GLU 22": "OE1" <-> "OE2" Residue "B ARG 33": "NH1" <-> "NH2" Residue "B ARG 81": "NH1" <-> "NH2" Residue "B ARG 153": "NH1" <-> "NH2" Residue "B ARG 179": "NH1" <-> "NH2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B GLU 377": "OE1" <-> "OE2" Residue "B ARG 387": "NH1" <-> "NH2" Residue "B GLU 419": "OE1" <-> "OE2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 81": "NH1" <-> "NH2" Residue "C ARG 153": "NH1" <-> "NH2" Residue "C ARG 179": "NH1" <-> "NH2" Residue "C GLU 257": "OE1" <-> "OE2" Residue "C GLU 267": "OE1" <-> "OE2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C ARG 373": "NH1" <-> "NH2" Residue "C ARG 387": "NH1" <-> "NH2" Residue "D GLU 26": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 81": "NH1" <-> "NH2" Residue "D GLU 151": "OE1" <-> "OE2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D GLU 169": "OE1" <-> "OE2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "D GLU 243": "OE1" <-> "OE2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D GLU 257": "OE1" <-> "OE2" Residue "D ARG 314": "NH1" <-> "NH2" Residue "D ARG 373": "NH1" <-> "NH2" Residue "E ARG 33": "NH1" <-> "NH2" Residue "E GLU 37": "OE1" <-> "OE2" Residue "E ARG 81": "NH1" <-> "NH2" Residue "E GLU 151": "OE1" <-> "OE2" Residue "E ARG 153": "NH1" <-> "NH2" Residue "E ARG 179": "NH1" <-> "NH2" Residue "E GLU 243": "OE1" <-> "OE2" Residue "E GLU 253": "OE1" <-> "OE2" Residue "E ARG 314": "NH1" <-> "NH2" Residue "E ARG 373": "NH1" <-> "NH2" Residue "E GLU 383": "OE1" <-> "OE2" Residue "E ARG 387": "NH1" <-> "NH2" Residue "F GLU 22": "OE1" <-> "OE2" Residue "F ARG 33": "NH1" <-> "NH2" Residue "F ARG 81": "NH1" <-> "NH2" Residue "F GLU 151": "OE1" <-> "OE2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 179": "NH1" <-> "NH2" Residue "F GLU 209": "OE1" <-> "OE2" Residue "F GLU 257": "OE1" <-> "OE2" Residue "F ARG 314": "NH1" <-> "NH2" Residue "F ARG 373": "NH1" <-> "NH2" Residue "F GLU 377": "OE1" <-> "OE2" Residue "F ARG 387": "NH1" <-> "NH2" Residue "G GLU 26": "OE1" <-> "OE2" Residue "G ARG 33": "NH1" <-> "NH2" Residue "G GLU 37": "OE1" <-> "OE2" Residue "G ARG 81": "NH1" <-> "NH2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 179": "NH1" <-> "NH2" Residue "G GLU 243": "OE1" <-> "OE2" Residue "G GLU 267": "OE1" <-> "OE2" Residue "G ARG 314": "NH1" <-> "NH2" Residue "G ARG 373": "NH1" <-> "NH2" Residue "G GLU 383": "OE1" <-> "OE2" Residue "G ARG 387": "NH1" <-> "NH2" Residue "G GLU 419": "OE1" <-> "OE2" Residue "J ARG 73": "NH1" <-> "NH2" Residue "J ARG 159": "NH1" <-> "NH2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "K ARG 73": "NH1" <-> "NH2" Residue "K GLU 130": "OE1" <-> "OE2" Residue "K ARG 159": "NH1" <-> "NH2" Residue "K GLU 204": "OE1" <-> "OE2" Residue "L ARG 73": "NH1" <-> "NH2" Residue "L ARG 159": "NH1" <-> "NH2" Residue "L GLU 191": "OE1" <-> "OE2" Residue "L GLU 204": "OE1" <-> "OE2" Residue "M ARG 60": "NH1" <-> "NH2" Residue "M ARG 73": "NH1" <-> "NH2" Residue "M ARG 159": "NH1" <-> "NH2" Residue "M PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 60": "NH1" <-> "NH2" Residue "N GLU 62": "OE1" <-> "OE2" Residue "N ARG 73": "NH1" <-> "NH2" Residue "N ARG 159": "NH1" <-> "NH2" Residue "O ARG 60": "NH1" <-> "NH2" Residue "O GLU 62": "OE1" <-> "OE2" Residue "O ARG 73": "NH1" <-> "NH2" Residue "O GLU 156": "OE1" <-> "OE2" Residue "O ARG 159": "NH1" <-> "NH2" Residue "P ARG 60": "NH1" <-> "NH2" Residue "P ARG 73": "NH1" <-> "NH2" Residue "P ARG 159": "NH1" <-> "NH2" Residue "Q ARG 73": "NH1" <-> "NH2" Residue "Q ARG 159": "NH1" <-> "NH2" Residue "Q GLU 191": "OE1" <-> "OE2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "R ARG 159": "NH1" <-> "NH2" Residue "S ARG 60": "NH1" <-> "NH2" Residue "S ARG 73": "NH1" <-> "NH2" Residue "S ARG 159": "NH1" <-> "NH2" Residue "T ARG 60": "NH1" <-> "NH2" Residue "T PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "T ARG 159": "NH1" <-> "NH2" Residue "T PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 191": "OE1" <-> "OE2" Residue "U ARG 60": "NH1" <-> "NH2" Residue "U ARG 73": "NH1" <-> "NH2" Residue "U ARG 159": "NH1" <-> "NH2" Residue "U GLU 191": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39416 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 3003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3003 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 16, 'TRANS': 362} Chain breaks: 2 Chain: "B" Number of atoms: 3173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3173 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 19, 'TRANS': 380} Chain breaks: 2 Chain: "C" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3117 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 17, 'TRANS': 374} Chain breaks: 1 Chain: "D" Number of atoms: 3029 Number of conformers: 1 Conformer: "" Number of residues, atoms: 385, 3029 Classifications: {'peptide': 385} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 16, 'TRANS': 368} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3322 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 20, 'TRANS': 401} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 3322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3322 Classifications: {'peptide': 422} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 20, 'TRANS': 401} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 2} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 3033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 382, 3033 Classifications: {'peptide': 382} Link IDs: {'PTRANS': 17, 'TRANS': 364} Chain breaks: 2 Chain: "H" Number of atoms: 1344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 1344 Classifications: {'RNA': 68} Modifications used: {'rna2p_pyr': 9, 'rna3p_pyr': 59} Link IDs: {'rna2p': 9, 'rna3p': 58} Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen planarities: 16 Chain: "J" Number of atoms: 1278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1278 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 145} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "K" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1410 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 162} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1279 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 146} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1532 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 177} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1532 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 177} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 1532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1532 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 177} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1410 Classifications: {'peptide': 174} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 11, 'TRANS': 162} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Q" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1030 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 121} Chain breaks: 4 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "R" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 955 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 111} Chain breaks: 5 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "S" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1415 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "T" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1415 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "U" Number of atoms: 1285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1285 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 146} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 19.64, per 1000 atoms: 0.50 Number of scatterers: 39416 At special positions: 0 Unit cell: (143.1, 161.65, 135.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 201 16.00 P 68 15.00 O 7543 8.00 N 6464 7.00 C 25140 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.02 Conformation dependent library (CDL) restraints added in 6.8 seconds 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8894 Finding SS restraints... Secondary structure from input PDB file: 207 helices and 50 sheets defined 42.4% alpha, 11.2% beta 0 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 12.37 Creating SS restraints... Processing helix chain 'A' and resid 27 through 35 Processing helix chain 'A' and resid 47 through 62 Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 103 through 107 removed outlier: 3.651A pdb=" N ASP A 106 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU A 107 " --> pdb=" O ILE A 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 103 through 107' Processing helix chain 'A' and resid 133 through 145 removed outlier: 3.912A pdb=" N TYR A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 166 Processing helix chain 'A' and resid 184 through 187 Processing helix chain 'A' and resid 188 through 205 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 217 through 221 Processing helix chain 'A' and resid 225 through 238 Processing helix chain 'A' and resid 241 through 246 removed outlier: 3.812A pdb=" N THR A 246 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 253 through 262 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 294 through 308 removed outlier: 3.519A pdb=" N HIS A 298 " --> pdb=" O ASN A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 341 Processing helix chain 'A' and resid 392 through 402 Processing helix chain 'A' and resid 411 through 420 Processing helix chain 'B' and resid 27 through 35 Processing helix chain 'B' and resid 47 through 62 Processing helix chain 'B' and resid 65 through 77 Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.880A pdb=" N LEU B 107 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL B 108 " --> pdb=" O PHE B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 145 removed outlier: 4.019A pdb=" N TYR B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 166 removed outlier: 3.617A pdb=" N LYS B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 187 Processing helix chain 'B' and resid 188 through 205 removed outlier: 3.524A pdb=" N THR B 192 " --> pdb=" O ASP B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 212 No H-bonds generated for 'chain 'B' and resid 210 through 212' Processing helix chain 'B' and resid 213 through 218 removed outlier: 4.144A pdb=" N THR B 217 " --> pdb=" O PHE B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 221 No H-bonds generated for 'chain 'B' and resid 219 through 221' Processing helix chain 'B' and resid 225 through 238 Processing helix chain 'B' and resid 241 through 246 removed outlier: 3.882A pdb=" N THR B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 253 through 262 Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 294 through 308 Processing helix chain 'B' and resid 324 through 341 removed outlier: 3.562A pdb=" N SER B 341 " --> pdb=" O ALA B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 385 removed outlier: 3.551A pdb=" N GLN B 385 " --> pdb=" O TRP B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 402 Processing helix chain 'B' and resid 411 through 420 Processing helix chain 'C' and resid 27 through 35 Processing helix chain 'C' and resid 47 through 62 Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.877A pdb=" N LEU C 107 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 146 removed outlier: 4.025A pdb=" N TYR C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 183 through 187 removed outlier: 3.545A pdb=" N GLY C 186 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 205 removed outlier: 3.856A pdb=" N THR C 192 " --> pdb=" O ASP C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 212 No H-bonds generated for 'chain 'C' and resid 210 through 212' Processing helix chain 'C' and resid 213 through 218 removed outlier: 4.316A pdb=" N THR C 217 " --> pdb=" O PHE C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 221 No H-bonds generated for 'chain 'C' and resid 219 through 221' Processing helix chain 'C' and resid 225 through 239 removed outlier: 3.723A pdb=" N GLY C 239 " --> pdb=" O CYS C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 249 removed outlier: 3.634A pdb=" N THR C 246 " --> pdb=" O THR C 242 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR C 247 " --> pdb=" O GLU C 243 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TRP C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE C 249 " --> pdb=" O VAL C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 262 removed outlier: 3.769A pdb=" N ASP C 256 " --> pdb=" O ARG C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 267 removed outlier: 3.851A pdb=" N GLU C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 278 Processing helix chain 'C' and resid 294 through 308 Processing helix chain 'C' and resid 324 through 341 Processing helix chain 'C' and resid 374 through 384 removed outlier: 3.585A pdb=" N TRP C 378 " --> pdb=" O ASP C 374 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 402 Processing helix chain 'C' and resid 411 through 420 Processing helix chain 'D' and resid 27 through 35 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 104 through 108 removed outlier: 3.895A pdb=" N LEU D 107 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL D 108 " --> pdb=" O PHE D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 104 through 108' Processing helix chain 'D' and resid 133 through 145 removed outlier: 3.620A pdb=" N TYR D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 180 through 187 removed outlier: 3.505A pdb=" N VAL D 184 " --> pdb=" O ILE D 181 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY D 186 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 205 Processing helix chain 'D' and resid 210 through 215 Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 225 through 239 removed outlier: 3.814A pdb=" N GLY D 239 " --> pdb=" O CYS D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 246 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 253 through 262 Processing helix chain 'D' and resid 263 through 267 removed outlier: 3.592A pdb=" N GLN D 266 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLU D 267 " --> pdb=" O PRO D 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 263 through 267' Processing helix chain 'D' and resid 274 through 278 Processing helix chain 'D' and resid 294 through 308 removed outlier: 3.714A pdb=" N HIS D 298 " --> pdb=" O ASN D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 341 removed outlier: 3.670A pdb=" N SER D 341 " --> pdb=" O ALA D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 383 Processing helix chain 'D' and resid 393 through 402 Processing helix chain 'D' and resid 411 through 420 Processing helix chain 'E' and resid 27 through 35 Processing helix chain 'E' and resid 47 through 62 Processing helix chain 'E' and resid 65 through 77 Processing helix chain 'E' and resid 104 through 108 removed outlier: 3.981A pdb=" N LEU E 107 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 145 removed outlier: 3.794A pdb=" N TYR E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 169 removed outlier: 4.499A pdb=" N LYS E 155 " --> pdb=" O GLU E 151 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE E 167 " --> pdb=" O GLN E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 187 removed outlier: 3.790A pdb=" N GLY E 186 " --> pdb=" O ASP E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 205 removed outlier: 3.639A pdb=" N THR E 192 " --> pdb=" O ASP E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 210 through 215 Processing helix chain 'E' and resid 217 through 221 Processing helix chain 'E' and resid 225 through 238 Processing helix chain 'E' and resid 241 through 248 removed outlier: 4.061A pdb=" N THR E 246 " --> pdb=" O THR E 242 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR E 247 " --> pdb=" O GLU E 243 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TRP E 248 " --> pdb=" O ASP E 244 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 262 removed outlier: 4.193A pdb=" N ASP E 256 " --> pdb=" O ARG E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 267 removed outlier: 4.093A pdb=" N GLU E 267 " --> pdb=" O PRO E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 278 Processing helix chain 'E' and resid 294 through 308 removed outlier: 3.692A pdb=" N HIS E 298 " --> pdb=" O ASN E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 341 removed outlier: 3.506A pdb=" N SER E 340 " --> pdb=" O TYR E 336 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER E 341 " --> pdb=" O ALA E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 385 Processing helix chain 'E' and resid 390 through 402 Processing helix chain 'E' and resid 411 through 420 Processing helix chain 'F' and resid 27 through 35 Processing helix chain 'F' and resid 47 through 62 Processing helix chain 'F' and resid 65 through 77 Processing helix chain 'F' and resid 104 through 108 removed outlier: 3.864A pdb=" N LEU F 107 " --> pdb=" O ILE F 104 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL F 108 " --> pdb=" O PHE F 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 104 through 108' Processing helix chain 'F' and resid 133 through 145 removed outlier: 3.650A pdb=" N TYR F 142 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 168 removed outlier: 3.846A pdb=" N ILE F 167 " --> pdb=" O GLN F 163 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 187 removed outlier: 3.620A pdb=" N GLY F 186 " --> pdb=" O ASP F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 205 Processing helix chain 'F' and resid 210 through 215 Processing helix chain 'F' and resid 217 through 221 Processing helix chain 'F' and resid 225 through 239 removed outlier: 3.670A pdb=" N GLY F 239 " --> pdb=" O CYS F 235 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 246 Processing helix chain 'F' and resid 247 through 249 No H-bonds generated for 'chain 'F' and resid 247 through 249' Processing helix chain 'F' and resid 253 through 262 removed outlier: 3.621A pdb=" N GLU F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 274 through 278 Processing helix chain 'F' and resid 294 through 308 Processing helix chain 'F' and resid 324 through 341 Processing helix chain 'F' and resid 374 through 384 Processing helix chain 'F' and resid 390 through 402 Processing helix chain 'F' and resid 411 through 420 Processing helix chain 'G' and resid 27 through 35 Processing helix chain 'G' and resid 47 through 62 Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 103 through 108 removed outlier: 3.921A pdb=" N LEU G 107 " --> pdb=" O ILE G 104 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL G 108 " --> pdb=" O PHE G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 129 through 145 removed outlier: 4.056A pdb=" N TRP G 133 " --> pdb=" O ALA G 129 " (cutoff:3.500A) Proline residue: G 135 - end of helix removed outlier: 3.741A pdb=" N TYR G 142 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG G 143 " --> pdb=" O LEU G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 164 Processing helix chain 'G' and resid 183 through 187 removed outlier: 3.508A pdb=" N GLY G 186 " --> pdb=" O ASP G 183 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 205 removed outlier: 3.748A pdb=" N THR G 192 " --> pdb=" O ASP G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 212 No H-bonds generated for 'chain 'G' and resid 210 through 212' Processing helix chain 'G' and resid 213 through 218 removed outlier: 4.187A pdb=" N THR G 217 " --> pdb=" O PHE G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 219 through 221 No H-bonds generated for 'chain 'G' and resid 219 through 221' Processing helix chain 'G' and resid 225 through 239 removed outlier: 3.752A pdb=" N THR G 238 " --> pdb=" O LEU G 234 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLY G 239 " --> pdb=" O CYS G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 246 removed outlier: 3.657A pdb=" N THR G 246 " --> pdb=" O THR G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 249 No H-bonds generated for 'chain 'G' and resid 247 through 249' Processing helix chain 'G' and resid 252 through 262 removed outlier: 3.773A pdb=" N ASP G 256 " --> pdb=" O ARG G 252 " (cutoff:3.500A) Processing helix chain 'G' and resid 294 through 308 Processing helix chain 'G' and resid 323 through 339 removed outlier: 4.181A pdb=" N LEU G 327 " --> pdb=" O GLU G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 374 through 384 Processing helix chain 'G' and resid 390 through 402 Processing helix chain 'G' and resid 411 through 421 Processing helix chain 'J' and resid 80 through 89 Processing helix chain 'J' and resid 90 through 93 Processing helix chain 'J' and resid 101 through 115 Processing helix chain 'J' and resid 119 through 123 Processing helix chain 'J' and resid 200 through 207 removed outlier: 3.519A pdb=" N LEU J 206 " --> pdb=" O GLN J 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 89 Processing helix chain 'K' and resid 90 through 93 removed outlier: 3.659A pdb=" N ASN K 93 " --> pdb=" O GLN K 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 90 through 93' Processing helix chain 'K' and resid 98 through 100 No H-bonds generated for 'chain 'K' and resid 98 through 100' Processing helix chain 'K' and resid 101 through 115 Processing helix chain 'K' and resid 119 through 123 Processing helix chain 'K' and resid 188 through 193 removed outlier: 3.852A pdb=" N MET K 193 " --> pdb=" O TRP K 190 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 205 Processing helix chain 'L' and resid 80 through 89 Processing helix chain 'L' and resid 90 through 93 removed outlier: 3.510A pdb=" N ASN L 93 " --> pdb=" O GLN L 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 90 through 93' Processing helix chain 'L' and resid 98 through 100 No H-bonds generated for 'chain 'L' and resid 98 through 100' Processing helix chain 'L' and resid 101 through 115 Processing helix chain 'L' and resid 119 through 123 Processing helix chain 'L' and resid 188 through 193 removed outlier: 3.714A pdb=" N MET L 193 " --> pdb=" O TRP L 190 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 208 Processing helix chain 'M' and resid 80 through 89 Processing helix chain 'M' and resid 101 through 115 Processing helix chain 'M' and resid 119 through 123 removed outlier: 3.607A pdb=" N LEU M 123 " --> pdb=" O PRO M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 193 removed outlier: 3.512A pdb=" N MET M 193 " --> pdb=" O TRP M 190 " (cutoff:3.500A) Processing helix chain 'M' and resid 200 through 208 removed outlier: 3.709A pdb=" N GLU M 204 " --> pdb=" O GLN M 200 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N PHE M 208 " --> pdb=" O GLU M 204 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 90 removed outlier: 4.307A pdb=" N GLN N 90 " --> pdb=" O ALA N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 115 Processing helix chain 'N' and resid 119 through 123 Processing helix chain 'N' and resid 188 through 193 removed outlier: 3.576A pdb=" N MET N 193 " --> pdb=" O TRP N 190 " (cutoff:3.500A) Processing helix chain 'N' and resid 200 through 205 Processing helix chain 'O' and resid 80 through 89 Processing helix chain 'O' and resid 90 through 93 removed outlier: 3.699A pdb=" N ASN O 93 " --> pdb=" O GLN O 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 90 through 93' Processing helix chain 'O' and resid 101 through 115 Processing helix chain 'O' and resid 119 through 123 Processing helix chain 'O' and resid 188 through 193 removed outlier: 3.503A pdb=" N MET O 193 " --> pdb=" O TRP O 190 " (cutoff:3.500A) Processing helix chain 'O' and resid 200 through 208 removed outlier: 4.090A pdb=" N LEU O 206 " --> pdb=" O GLN O 202 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N PHE O 208 " --> pdb=" O GLU O 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 90 removed outlier: 3.529A pdb=" N VAL P 84 " --> pdb=" O SER P 80 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN P 90 " --> pdb=" O ALA P 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 93 No H-bonds generated for 'chain 'P' and resid 91 through 93' Processing helix chain 'P' and resid 101 through 115 Processing helix chain 'P' and resid 120 through 123 Processing helix chain 'P' and resid 189 through 193 removed outlier: 3.563A pdb=" N MET P 193 " --> pdb=" O TRP P 190 " (cutoff:3.500A) Processing helix chain 'P' and resid 200 through 207 Processing helix chain 'Q' and resid 80 through 89 Processing helix chain 'Q' and resid 98 through 100 No H-bonds generated for 'chain 'Q' and resid 98 through 100' Processing helix chain 'Q' and resid 101 through 115 Processing helix chain 'Q' and resid 200 through 205 Processing helix chain 'Q' and resid 206 through 208 No H-bonds generated for 'chain 'Q' and resid 206 through 208' Processing helix chain 'R' and resid 80 through 89 Processing helix chain 'R' and resid 101 through 115 Processing helix chain 'R' and resid 201 through 208 removed outlier: 3.868A pdb=" N LEU R 206 " --> pdb=" O GLN R 202 " (cutoff:3.500A) Processing helix chain 'S' and resid 80 through 90 removed outlier: 4.020A pdb=" N GLN S 90 " --> pdb=" O ALA S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 93 No H-bonds generated for 'chain 'S' and resid 91 through 93' Processing helix chain 'S' and resid 101 through 115 Processing helix chain 'S' and resid 189 through 193 removed outlier: 3.677A pdb=" N MET S 193 " --> pdb=" O TRP S 190 " (cutoff:3.500A) Processing helix chain 'S' and resid 200 through 205 removed outlier: 3.641A pdb=" N GLY S 205 " --> pdb=" O ILE S 201 " (cutoff:3.500A) Processing helix chain 'S' and resid 206 through 208 No H-bonds generated for 'chain 'S' and resid 206 through 208' Processing helix chain 'T' and resid 80 through 89 Processing helix chain 'T' and resid 98 through 100 No H-bonds generated for 'chain 'T' and resid 98 through 100' Processing helix chain 'T' and resid 101 through 115 Processing helix chain 'T' and resid 189 through 193 Processing helix chain 'T' and resid 200 through 208 removed outlier: 3.511A pdb=" N LEU T 206 " --> pdb=" O GLN T 202 " (cutoff:3.500A) Processing helix chain 'U' and resid 80 through 89 Processing helix chain 'U' and resid 98 through 100 No H-bonds generated for 'chain 'U' and resid 98 through 100' Processing helix chain 'U' and resid 101 through 115 removed outlier: 3.526A pdb=" N HIS U 115 " --> pdb=" O ILE U 111 " (cutoff:3.500A) Processing helix chain 'U' and resid 189 through 193 removed outlier: 3.501A pdb=" N MET U 193 " --> pdb=" O TRP U 190 " (cutoff:3.500A) Processing helix chain 'U' and resid 202 through 208 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.715A pdb=" N ILE A 42 " --> pdb=" O LYS A 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 348 through 349 Processing sheet with id=AA3, first strand: chain 'B' and resid 39 through 42 removed outlier: 5.875A pdb=" N LEU B 40 " --> pdb=" O LYS B 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 89 through 90 Processing sheet with id=AA5, first strand: chain 'C' and resid 41 through 42 Processing sheet with id=AA6, first strand: chain 'D' and resid 39 through 42 removed outlier: 6.152A pdb=" N LEU D 40 " --> pdb=" O LYS D 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'D' and resid 348 through 349 Processing sheet with id=AA8, first strand: chain 'E' and resid 6 through 7 removed outlier: 3.726A pdb=" N THR E 12 " --> pdb=" O ARG E 7 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 41 through 42 removed outlier: 3.788A pdb=" N ILE E 42 " --> pdb=" O LYS E 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'E' and resid 89 through 90 Processing sheet with id=AB2, first strand: chain 'E' and resid 348 through 349 Processing sheet with id=AB3, first strand: chain 'F' and resid 39 through 42 removed outlier: 6.154A pdb=" N LEU F 40 " --> pdb=" O LYS F 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'F' and resid 89 through 90 Processing sheet with id=AB5, first strand: chain 'G' and resid 39 through 42 removed outlier: 6.009A pdb=" N LEU G 40 " --> pdb=" O LYS G 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'G' and resid 89 through 90 Processing sheet with id=AB7, first strand: chain 'J' and resid 136 through 137 removed outlier: 4.045A pdb=" N GLY J 137 " --> pdb=" O PHE J 66 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHE J 66 " --> pdb=" O GLY J 137 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER J 178 " --> pdb=" O ARG J 65 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 70 through 73 removed outlier: 3.680A pdb=" N ALA J 133 " --> pdb=" O MET J 70 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 137 through 143 Processing sheet with id=AC1, first strand: chain 'K' and resid 130 through 134 removed outlier: 3.531A pdb=" N ALA K 133 " --> pdb=" O MET K 70 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU K 156 " --> pdb=" O PHE K 175 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'K' and resid 211 through 214 removed outlier: 6.890A pdb=" N ILE K 211 " --> pdb=" O ASP K 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 130 through 141 Processing sheet with id=AC4, first strand: chain 'L' and resid 156 through 158 removed outlier: 3.577A pdb=" N GLU L 156 " --> pdb=" O PHE L 175 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE L 158 " --> pdb=" O PHE L 173 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 162 through 163 removed outlier: 3.637A pdb=" N GLY L 169 " --> pdb=" O PHE L 162 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'M' and resid 130 through 143 removed outlier: 3.809A pdb=" N LEU M 141 " --> pdb=" O GLU M 62 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU M 62 " --> pdb=" O LEU M 141 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 130 through 143 removed outlier: 3.809A pdb=" N LEU M 141 " --> pdb=" O GLU M 62 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU M 62 " --> pdb=" O LEU M 141 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 156 through 158 removed outlier: 3.677A pdb=" N PHE M 158 " --> pdb=" O PHE M 173 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 212 through 214 removed outlier: 3.601A pdb=" N SER M 213 " --> pdb=" O VAL M 221 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL M 221 " --> pdb=" O SER M 213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'N' and resid 130 through 143 removed outlier: 3.512A pdb=" N ALA N 133 " --> pdb=" O MET N 70 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU N 62 " --> pdb=" O LEU N 141 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU N 156 " --> pdb=" O PHE N 175 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 130 through 143 removed outlier: 3.512A pdb=" N ALA N 133 " --> pdb=" O MET N 70 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU N 62 " --> pdb=" O LEU N 141 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 211 through 214 removed outlier: 6.930A pdb=" N ILE N 211 " --> pdb=" O ASP N 223 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER N 213 " --> pdb=" O VAL N 221 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 130 through 143 removed outlier: 3.534A pdb=" N LEU O 141 " --> pdb=" O GLU O 62 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU O 62 " --> pdb=" O LEU O 141 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N PHE O 175 " --> pdb=" O GLU O 156 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLU O 156 " --> pdb=" O PHE O 175 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 130 through 143 removed outlier: 3.534A pdb=" N LEU O 141 " --> pdb=" O GLU O 62 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU O 62 " --> pdb=" O LEU O 141 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'O' and resid 211 through 214 removed outlier: 6.724A pdb=" N ILE O 211 " --> pdb=" O ASP O 223 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'P' and resid 137 through 143 removed outlier: 3.830A pdb=" N GLU P 62 " --> pdb=" O LEU P 141 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'P' and resid 117 through 118 removed outlier: 3.607A pdb=" N TYR P 132 " --> pdb=" O GLN P 117 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL P 72 " --> pdb=" O TYR P 131 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA P 133 " --> pdb=" O MET P 70 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR P 174 " --> pdb=" O LYS P 69 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE P 158 " --> pdb=" O PHE P 173 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'P' and resid 210 through 213 removed outlier: 7.174A pdb=" N ILE P 211 " --> pdb=" O ASP P 223 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'Q' and resid 117 through 118 removed outlier: 3.505A pdb=" N TYR Q 132 " --> pdb=" O GLN Q 117 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'Q' and resid 210 through 212 removed outlier: 6.923A pdb=" N ILE Q 211 " --> pdb=" O ASP Q 223 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'R' and resid 130 through 135 removed outlier: 3.501A pdb=" N ALA R 133 " --> pdb=" O MET R 70 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 117 through 118 removed outlier: 3.548A pdb=" N GLN S 117 " --> pdb=" O TYR S 132 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL S 72 " --> pdb=" O TYR S 131 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY S 137 " --> pdb=" O PHE S 66 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE S 66 " --> pdb=" O GLY S 137 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS S 139 " --> pdb=" O PHE S 64 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR S 174 " --> pdb=" O LYS S 69 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N PHE S 158 " --> pdb=" O PHE S 173 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE S 175 " --> pdb=" O GLU S 156 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'S' and resid 117 through 118 removed outlier: 3.548A pdb=" N GLN S 117 " --> pdb=" O TYR S 132 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL S 72 " --> pdb=" O TYR S 131 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N GLY S 137 " --> pdb=" O PHE S 66 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE S 66 " --> pdb=" O GLY S 137 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N CYS S 139 " --> pdb=" O PHE S 64 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 162 through 163 removed outlier: 4.095A pdb=" N GLY S 169 " --> pdb=" O PHE S 162 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'S' and resid 210 through 213 removed outlier: 6.694A pdb=" N ILE S 211 " --> pdb=" O ASP S 223 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER S 213 " --> pdb=" O VAL S 221 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL S 221 " --> pdb=" O SER S 213 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'T' and resid 117 through 118 removed outlier: 3.599A pdb=" N TYR T 132 " --> pdb=" O GLN T 117 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA T 133 " --> pdb=" O MET T 70 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY T 137 " --> pdb=" O PHE T 66 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 117 through 118 removed outlier: 3.599A pdb=" N TYR T 132 " --> pdb=" O GLN T 117 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA T 133 " --> pdb=" O MET T 70 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY T 137 " --> pdb=" O PHE T 66 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'T' and resid 162 through 163 Processing sheet with id=AF2, first strand: chain 'T' and resid 210 through 213 removed outlier: 6.741A pdb=" N ILE T 211 " --> pdb=" O ASP T 223 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N SER T 213 " --> pdb=" O VAL T 221 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL T 221 " --> pdb=" O SER T 213 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'U' and resid 60 through 65 removed outlier: 3.709A pdb=" N HIS U 143 " --> pdb=" O ARG U 60 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU U 62 " --> pdb=" O LEU U 141 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U' and resid 71 through 73 Processing sheet with id=AF5, first strand: chain 'U' and resid 162 through 163 1441 hydrogen bonds defined for protein. 3915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 13.23 Time building geometry restraints manager: 16.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11012 1.34 - 1.45: 7412 1.45 - 1.57: 21574 1.57 - 1.69: 135 1.69 - 1.81: 359 Bond restraints: 40492 Sorted by residual: bond pdb=" N ASN A 190 " pdb=" CA ASN A 190 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.05e+00 bond pdb=" N ASP A 180 " pdb=" CA ASP A 180 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.25e-02 6.40e+03 5.93e+00 bond pdb=" N TYR J 95 " pdb=" CA TYR J 95 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.28e-02 6.10e+03 5.79e+00 bond pdb=" N LYS T 207 " pdb=" CA LYS T 207 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.28e-02 6.10e+03 5.14e+00 bond pdb=" C LYS C 388 " pdb=" N PRO C 389 " ideal model delta sigma weight residual 1.332 1.361 -0.029 1.30e-02 5.92e+03 5.10e+00 ... (remaining 40487 not shown) Histogram of bond angle deviations from ideal: 98.89 - 105.91: 1281 105.91 - 112.94: 21128 112.94 - 119.97: 13906 119.97 - 127.00: 18207 127.00 - 134.02: 517 Bond angle restraints: 55039 Sorted by residual: angle pdb=" N ILE M 96 " pdb=" CA ILE M 96 " pdb=" C ILE M 96 " ideal model delta sigma weight residual 113.53 108.10 5.43 9.80e-01 1.04e+00 3.07e+01 angle pdb=" N PHE T 208 " pdb=" CA PHE T 208 " pdb=" C PHE T 208 " ideal model delta sigma weight residual 113.19 107.06 6.13 1.19e+00 7.06e-01 2.66e+01 angle pdb=" N ILE E 8 " pdb=" CA ILE E 8 " pdb=" C ILE E 8 " ideal model delta sigma weight residual 106.21 111.60 -5.39 1.07e+00 8.73e-01 2.54e+01 angle pdb=" N TYR E 152 " pdb=" CA TYR E 152 " pdb=" C TYR E 152 " ideal model delta sigma weight residual 113.55 107.32 6.23 1.26e+00 6.30e-01 2.45e+01 angle pdb=" N ILE K 96 " pdb=" CA ILE K 96 " pdb=" C ILE K 96 " ideal model delta sigma weight residual 113.53 109.00 4.53 9.80e-01 1.04e+00 2.14e+01 ... (remaining 55034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.73: 23764 35.73 - 71.47: 545 71.47 - 107.20: 30 107.20 - 142.93: 2 142.93 - 178.67: 17 Dihedral angle restraints: 24358 sinusoidal: 10494 harmonic: 13864 Sorted by residual: dihedral pdb=" O4' U H 127 " pdb=" C1' U H 127 " pdb=" N1 U H 127 " pdb=" C2 U H 127 " ideal model delta sinusoidal sigma weight residual 200.00 38.88 161.12 1 1.50e+01 4.44e-03 8.30e+01 dihedral pdb=" O4' U H 118 " pdb=" C1' U H 118 " pdb=" N1 U H 118 " pdb=" C2 U H 118 " ideal model delta sinusoidal sigma weight residual -160.00 -2.93 -157.07 1 1.50e+01 4.44e-03 8.20e+01 dihedral pdb=" O4' U H 469 " pdb=" C1' U H 469 " pdb=" N1 U H 469 " pdb=" C2 U H 469 " ideal model delta sinusoidal sigma weight residual 200.00 45.52 154.48 1 1.50e+01 4.44e-03 8.12e+01 ... (remaining 24355 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 5036 0.053 - 0.105: 882 0.105 - 0.158: 109 0.158 - 0.210: 6 0.210 - 0.263: 1 Chirality restraints: 6034 Sorted by residual: chirality pdb=" CA LYS C 388 " pdb=" N LYS C 388 " pdb=" C LYS C 388 " pdb=" CB LYS C 388 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" C3' U H 129 " pdb=" C4' U H 129 " pdb=" O3' U H 129 " pdb=" C2' U H 129 " both_signs ideal model delta sigma weight residual False -2.74 -2.55 -0.19 2.00e-01 2.50e+01 9.26e-01 chirality pdb=" C3' U H 454 " pdb=" C4' U H 454 " pdb=" O3' U H 454 " pdb=" C2' U H 454 " both_signs ideal model delta sigma weight residual False -2.48 -2.29 -0.19 2.00e-01 2.50e+01 8.60e-01 ... (remaining 6031 not shown) Planarity restraints: 6770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO U 149 " 0.060 5.00e-02 4.00e+02 9.12e-02 1.33e+01 pdb=" N PRO U 150 " -0.158 5.00e-02 4.00e+02 pdb=" CA PRO U 150 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO U 150 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE J 148 " 0.044 5.00e-02 4.00e+02 6.66e-02 7.09e+00 pdb=" N PRO J 149 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO J 149 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO J 149 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE U 148 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO U 149 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO U 149 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO U 149 " 0.034 5.00e-02 4.00e+02 ... (remaining 6767 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2829 2.74 - 3.28: 40924 3.28 - 3.82: 65998 3.82 - 4.36: 78968 4.36 - 4.90: 132552 Nonbonded interactions: 321271 Sorted by model distance: nonbonded pdb=" OD1 ASN E 251 " pdb=" OG SER E 326 " model vdw 2.196 2.440 nonbonded pdb=" OH TYR A 336 " pdb=" OD2 ASP A 392 " model vdw 2.199 2.440 nonbonded pdb=" OD1 ASP D 199 " pdb=" OH TYR D 277 " model vdw 2.200 2.440 nonbonded pdb=" OD1 ASN D 94 " pdb=" NZ LYS D 97 " model vdw 2.200 2.520 nonbonded pdb=" OH TYR D 336 " pdb=" OD2 ASP D 392 " model vdw 2.203 2.440 ... (remaining 321266 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 22 through 164 or resid 173 through 319 or resid 327 throu \ gh 339 or resid 371 or resid 373 or resid 392 through 421)) selection = (chain 'B' and (resid 22 through 164 or resid 173 through 319 or resid 327 throu \ gh 339 or resid 371 or resid 373 or resid 392 through 421)) selection = (chain 'C' and (resid 22 through 164 or resid 173 through 319 or resid 327 throu \ gh 339 or resid 385 or resid 387 or resid 392 through 421)) selection = (chain 'D' and (resid 22 through 164 or resid 173 through 339 or resid 371 or re \ sid 373 or resid 392 through 421)) selection = (chain 'E' and (resid 22 through 164 or resid 173 through 319 or resid 327 throu \ gh 339 or resid 371 or resid 373 or resid 392 through 421)) selection = (chain 'F' and (resid 22 through 164 or resid 173 through 319 or resid 327 throu \ gh 339 or resid 371 or resid 373 or resid 392 through 421)) selection = (chain 'G' and (resid 22 through 319 or resid 327 through 339 or resid 385 or re \ sid 387 or resid 392 through 421)) } ncs_group { reference = (chain 'J' and (resid 62 through 122 or resid 127 through 143 or resid 148 throu \ gh 162 or resid 169 through 194 or resid 201 through 212 or resid 220 through 22 \ 5)) selection = (chain 'K' and (resid 62 through 122 or resid 127 through 143 or resid 148 throu \ gh 162 or resid 169 through 180 or resid 186 through 194 or resid 201 through 21 \ 2 or resid 220 through 225)) selection = (chain 'L' and (resid 62 through 122 or resid 127 through 162 or resid 169 throu \ gh 180 or resid 186 through 194 or resid 201 through 212 or resid 220 through 22 \ 5)) selection = (chain 'P' and (resid 62 through 122 or resid 127 through 143 or resid 148 throu \ gh 180 or resid 186 through 194 or resid 201 through 212 or resid 220 through 22 \ 5)) selection = (chain 'S' and (resid 62 through 143 or resid 148 through 162 or resid 169 throu \ gh 180 or resid 186 through 194 or resid 201 through 212 or resid 220 through 22 \ 5)) selection = (chain 'T' and (resid 62 through 143 or resid 148 through 162 or resid 169 throu \ gh 180 or resid 186 through 194 or resid 201 through 212 or resid 220 through 22 \ 5)) selection = (chain 'U' and (resid 62 through 143 or resid 148 through 162 or resid 169 throu \ gh 180 or resid 186 through 225)) } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = (chain 'Q' and (resid 66 through 178 or resid 192 through 195 or resid 200 throu \ gh 211 or resid 224 through 229)) selection = (chain 'R' and (resid 66 through 137 or resid 153 through 229)) } 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: 0.160 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: 3.360 Check model and map are aligned: 0.560 Set scattering table: 0.340 Process input model: 104.670 Find NCS groups from input model: 3.370 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 40492 Z= 0.177 Angle : 0.651 9.645 55039 Z= 0.374 Chirality : 0.040 0.263 6034 Planarity : 0.005 0.091 6770 Dihedral : 15.935 178.669 15464 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.12 % Allowed : 0.27 % Favored : 99.61 % 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: -1.19 (0.12), residues: 4672 helix: 0.57 (0.13), residues: 1714 sheet: -1.96 (0.23), residues: 516 loop : -1.53 (0.12), residues: 2442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 248 HIS 0.005 0.001 HIS U 115 PHE 0.025 0.001 PHE R 228 TYR 0.037 0.001 TYR D 54 ARG 0.014 0.001 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1108 time to evaluate : 4.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 TYR cc_start: 0.8476 (t80) cc_final: 0.8140 (t80) REVERT: A 170 GLN cc_start: 0.7964 (mp10) cc_final: 0.7739 (mp10) REVERT: A 257 GLU cc_start: 0.7056 (mt-10) cc_final: 0.6807 (mt-10) REVERT: A 312 ARG cc_start: 0.8897 (tmt-80) cc_final: 0.8667 (tmt-80) REVERT: A 324 TYR cc_start: 0.7865 (m-10) cc_final: 0.7646 (m-10) REVERT: B 1 MET cc_start: 0.4238 (mmp) cc_final: 0.3678 (mmp) REVERT: B 33 ARG cc_start: 0.7926 (mtm110) cc_final: 0.7155 (ttt180) REVERT: B 154 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8284 (tptp) REVERT: B 158 ASP cc_start: 0.7913 (m-30) cc_final: 0.7307 (m-30) REVERT: B 165 LYS cc_start: 0.8756 (mttm) cc_final: 0.8476 (mttt) REVERT: C 1 MET cc_start: 0.5568 (mmm) cc_final: 0.5191 (mmm) REVERT: C 4 THR cc_start: 0.9218 (t) cc_final: 0.8985 (m) REVERT: C 7 ARG cc_start: 0.7701 (ttt90) cc_final: 0.7280 (ttt180) REVERT: C 394 MET cc_start: 0.7303 (mmm) cc_final: 0.7051 (mpp) REVERT: D 154 LYS cc_start: 0.8893 (tptm) cc_final: 0.8643 (tppp) REVERT: D 394 MET cc_start: 0.6194 (mmp) cc_final: 0.5937 (mmp) REVERT: D 411 THR cc_start: 0.8610 (p) cc_final: 0.8399 (p) REVERT: F 1 MET cc_start: 0.5855 (mmm) cc_final: 0.4699 (mmm) REVERT: F 74 TYR cc_start: 0.8949 (t80) cc_final: 0.8735 (t80) REVERT: F 102 ILE cc_start: 0.8092 (tt) cc_final: 0.7892 (pt) REVERT: F 258 MET cc_start: 0.7939 (mmm) cc_final: 0.7411 (tpp) REVERT: F 377 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7805 (tt0) REVERT: F 402 MET cc_start: 0.8198 (ptm) cc_final: 0.7938 (ptp) REVERT: G 236 LYS cc_start: 0.8162 (tttm) cc_final: 0.7716 (tmtt) REVERT: G 324 TYR cc_start: 0.7413 (m-80) cc_final: 0.7088 (m-80) REVERT: J 81 TYR cc_start: 0.8126 (t80) cc_final: 0.7625 (t80) REVERT: J 168 LYS cc_start: 0.8453 (mmtm) cc_final: 0.8046 (mptt) REVERT: L 206 LEU cc_start: 0.8658 (tp) cc_final: 0.8406 (tp) REVERT: N 162 PHE cc_start: 0.9003 (p90) cc_final: 0.8768 (p90) REVERT: N 217 THR cc_start: 0.8131 (m) cc_final: 0.7929 (m) REVERT: P 74 SER cc_start: 0.6466 (t) cc_final: 0.6240 (t) REVERT: P 106 LYS cc_start: 0.8546 (mttt) cc_final: 0.8325 (mttp) REVERT: P 179 ASP cc_start: 0.7736 (m-30) cc_final: 0.7386 (m-30) REVERT: Q 101 LYS cc_start: 0.7846 (mtpt) cc_final: 0.7610 (mtpt) REVERT: S 140 PHE cc_start: 0.7592 (p90) cc_final: 0.6980 (p90) REVERT: S 207 LYS cc_start: 0.7700 (pttm) cc_final: 0.7386 (pttm) REVERT: T 76 LYS cc_start: 0.8045 (pttp) cc_final: 0.7592 (ptpt) REVERT: T 192 TYR cc_start: 0.7866 (m-80) cc_final: 0.7563 (m-80) REVERT: U 151 MET cc_start: 0.8038 (mpp) cc_final: 0.7082 (mpp) outliers start: 5 outliers final: 2 residues processed: 1109 average time/residue: 0.5114 time to fit residues: 910.8058 Evaluate side-chains 968 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 966 time to evaluate : 4.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 388 LYS Chi-restraints excluded: chain L residue 183 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 398 optimal weight: 8.9990 chunk 357 optimal weight: 10.0000 chunk 198 optimal weight: 20.0000 chunk 122 optimal weight: 7.9990 chunk 241 optimal weight: 6.9990 chunk 191 optimal weight: 0.9990 chunk 369 optimal weight: 2.9990 chunk 143 optimal weight: 9.9990 chunk 224 optimal weight: 0.9980 chunk 275 optimal weight: 2.9990 chunk 428 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 318 GLN ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 260 GLN D 294 ASN ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 GLN E 294 ASN F 94 ASN F 302 GLN ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN ** G 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 198 GLN M 163 ASN N 90 GLN P 115 HIS ** S 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 40492 Z= 0.244 Angle : 0.616 8.426 55039 Z= 0.321 Chirality : 0.041 0.226 6034 Planarity : 0.005 0.063 6770 Dihedral : 14.270 179.168 6280 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 1.65 % Allowed : 10.51 % Favored : 87.83 % 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: -1.17 (0.12), residues: 4672 helix: 0.53 (0.13), residues: 1757 sheet: -1.72 (0.22), residues: 549 loop : -1.55 (0.12), residues: 2366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP G 88 HIS 0.006 0.001 HIS U 115 PHE 0.030 0.002 PHE R 228 TYR 0.029 0.001 TYR T 81 ARG 0.010 0.001 ARG D 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 993 time to evaluate : 4.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8977 (tptt) cc_final: 0.8704 (tptt) REVERT: A 258 MET cc_start: 0.7338 (tpp) cc_final: 0.6881 (tpp) REVERT: A 354 LYS cc_start: 0.7085 (mttt) cc_final: 0.6811 (ttmt) REVERT: B 1 MET cc_start: 0.4288 (mmp) cc_final: 0.3587 (mmp) REVERT: B 33 ARG cc_start: 0.7947 (mtm110) cc_final: 0.7364 (ttt180) REVERT: B 47 SER cc_start: 0.8957 (OUTLIER) cc_final: 0.8676 (t) REVERT: B 154 LYS cc_start: 0.8539 (ttpt) cc_final: 0.8267 (tptp) REVERT: B 158 ASP cc_start: 0.7917 (m-30) cc_final: 0.7293 (m-30) REVERT: B 165 LYS cc_start: 0.8896 (mttm) cc_final: 0.8679 (mttt) REVERT: B 236 LYS cc_start: 0.8771 (ttpt) cc_final: 0.8443 (tmmt) REVERT: B 297 PHE cc_start: 0.8547 (t80) cc_final: 0.8270 (t80) REVERT: C 8 ILE cc_start: 0.7407 (pt) cc_final: 0.7121 (pt) REVERT: C 51 LEU cc_start: 0.8339 (mt) cc_final: 0.7799 (mt) REVERT: C 394 MET cc_start: 0.6958 (mmm) cc_final: 0.6579 (mpp) REVERT: C 419 GLU cc_start: 0.8281 (tm-30) cc_final: 0.8071 (tm-30) REVERT: D 54 TYR cc_start: 0.8725 (m-80) cc_final: 0.8498 (m-80) REVERT: D 154 LYS cc_start: 0.8941 (tptm) cc_final: 0.8654 (tppp) REVERT: D 158 ASP cc_start: 0.8164 (m-30) cc_final: 0.7929 (m-30) REVERT: D 253 GLU cc_start: 0.8168 (pm20) cc_final: 0.7961 (pm20) REVERT: E 297 PHE cc_start: 0.8445 (t80) cc_final: 0.7962 (t80) REVERT: F 1 MET cc_start: 0.5673 (mmm) cc_final: 0.4542 (mmm) REVERT: F 94 ASN cc_start: 0.8471 (OUTLIER) cc_final: 0.8197 (t0) REVERT: F 149 MET cc_start: 0.6732 (mtp) cc_final: 0.6457 (mtp) REVERT: F 258 MET cc_start: 0.8018 (mmm) cc_final: 0.7442 (tpp) REVERT: F 377 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7849 (tt0) REVERT: F 402 MET cc_start: 0.8190 (ptm) cc_final: 0.7939 (ptp) REVERT: G 151 GLU cc_start: 0.7459 (tp30) cc_final: 0.6989 (tp30) REVERT: G 236 LYS cc_start: 0.8198 (tttm) cc_final: 0.7848 (tmtt) REVERT: J 81 TYR cc_start: 0.8155 (t80) cc_final: 0.7946 (t80) REVERT: L 98 MET cc_start: 0.4210 (tpt) cc_final: 0.3819 (tpt) REVERT: L 193 MET cc_start: 0.8152 (mpp) cc_final: 0.7325 (mpp) REVERT: L 206 LEU cc_start: 0.8614 (tp) cc_final: 0.8389 (tp) REVERT: N 184 GLU cc_start: 0.7348 (tp30) cc_final: 0.6873 (tp30) REVERT: N 193 MET cc_start: 0.8479 (mpp) cc_final: 0.7555 (mpp) REVERT: O 144 ARG cc_start: 0.8578 (mtm-85) cc_final: 0.8279 (mtm-85) REVERT: P 74 SER cc_start: 0.6138 (t) cc_final: 0.5899 (t) REVERT: P 151 MET cc_start: 0.8703 (mtm) cc_final: 0.7988 (mtt) REVERT: P 179 ASP cc_start: 0.7843 (m-30) cc_final: 0.7515 (m-30) REVERT: P 224 GLN cc_start: 0.7194 (pm20) cc_final: 0.6810 (pm20) REVERT: Q 167 TYR cc_start: 0.6944 (m-80) cc_final: 0.6692 (m-80) REVERT: S 140 PHE cc_start: 0.7510 (p90) cc_final: 0.6789 (p90) REVERT: U 151 MET cc_start: 0.8046 (mpp) cc_final: 0.7051 (mpp) outliers start: 68 outliers final: 45 residues processed: 1024 average time/residue: 0.5460 time to fit residues: 911.8706 Evaluate side-chains 987 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 940 time to evaluate : 4.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 162 ASN Chi-restraints excluded: chain B residue 164 CYS Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 273 SER Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 388 LYS Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain E residue 210 CYS Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 94 ASN Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 89 SER Chi-restraints excluded: chain M residue 163 ASN Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 221 VAL Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 170 THR Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 58 SER Chi-restraints excluded: chain U residue 88 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 238 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 356 optimal weight: 8.9990 chunk 291 optimal weight: 5.9990 chunk 118 optimal weight: 0.5980 chunk 429 optimal weight: 0.0980 chunk 463 optimal weight: 6.9990 chunk 382 optimal weight: 6.9990 chunk 425 optimal weight: 8.9990 chunk 146 optimal weight: 9.9990 chunk 344 optimal weight: 5.9990 overall best weight: 3.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN A 294 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 395 GLN ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN N 90 GLN ** S 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 40492 Z= 0.294 Angle : 0.615 9.047 55039 Z= 0.319 Chirality : 0.042 0.259 6034 Planarity : 0.005 0.058 6770 Dihedral : 14.251 179.725 6280 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 2.28 % Allowed : 13.33 % Favored : 84.39 % 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: -1.20 (0.12), residues: 4672 helix: 0.43 (0.13), residues: 1778 sheet: -1.44 (0.22), residues: 575 loop : -1.60 (0.12), residues: 2319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 381 HIS 0.005 0.001 HIS L 115 PHE 0.031 0.002 PHE B 171 TYR 0.027 0.001 TYR A 56 ARG 0.006 0.000 ARG N 144 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1064 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 970 time to evaluate : 4.721 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8951 (tptt) cc_final: 0.8559 (tptp) REVERT: A 253 GLU cc_start: 0.6876 (pm20) cc_final: 0.6652 (pm20) REVERT: A 258 MET cc_start: 0.7477 (tpp) cc_final: 0.7064 (tpp) REVERT: A 354 LYS cc_start: 0.7126 (mttt) cc_final: 0.6903 (ttmt) REVERT: B 1 MET cc_start: 0.4377 (mmp) cc_final: 0.3608 (mmp) REVERT: B 47 SER cc_start: 0.8976 (OUTLIER) cc_final: 0.8684 (t) REVERT: B 154 LYS cc_start: 0.8582 (ttpt) cc_final: 0.8232 (tptp) REVERT: B 158 ASP cc_start: 0.7943 (m-30) cc_final: 0.7281 (m-30) REVERT: B 165 LYS cc_start: 0.8859 (mttm) cc_final: 0.8657 (mttt) REVERT: B 297 PHE cc_start: 0.8682 (t80) cc_final: 0.8426 (t80) REVERT: C 8 ILE cc_start: 0.7351 (pt) cc_final: 0.7109 (pt) REVERT: C 51 LEU cc_start: 0.8419 (mt) cc_final: 0.7973 (mt) REVERT: C 192 THR cc_start: 0.8289 (p) cc_final: 0.7915 (p) REVERT: C 200 MET cc_start: 0.8228 (ttm) cc_final: 0.8017 (ttm) REVERT: C 394 MET cc_start: 0.6988 (mmm) cc_final: 0.6608 (mpp) REVERT: C 409 GLU cc_start: 0.8263 (tm-30) cc_final: 0.8043 (tm-30) REVERT: C 419 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7997 (tm-30) REVERT: D 54 TYR cc_start: 0.8714 (m-80) cc_final: 0.8498 (m-80) REVERT: D 154 LYS cc_start: 0.8976 (tptm) cc_final: 0.8702 (tppp) REVERT: D 158 ASP cc_start: 0.8239 (m-30) cc_final: 0.7963 (m-30) REVERT: E 83 LYS cc_start: 0.9000 (ttmm) cc_final: 0.8774 (ttmm) REVERT: E 253 GLU cc_start: 0.8124 (pm20) cc_final: 0.7895 (pm20) REVERT: E 262 MET cc_start: 0.8208 (mtt) cc_final: 0.7582 (mtt) REVERT: F 1 MET cc_start: 0.5707 (mmm) cc_final: 0.4455 (mmm) REVERT: F 26 GLU cc_start: 0.7556 (tt0) cc_final: 0.7297 (tt0) REVERT: F 204 MET cc_start: 0.8874 (tpt) cc_final: 0.8610 (tpt) REVERT: F 240 MET cc_start: 0.8597 (mtp) cc_final: 0.7907 (ttm) REVERT: F 258 MET cc_start: 0.7970 (mmm) cc_final: 0.7143 (tpt) REVERT: F 377 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7848 (tt0) REVERT: G 236 LYS cc_start: 0.8322 (tttm) cc_final: 0.7981 (tmtt) REVERT: J 68 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6261 (mp) REVERT: J 81 TYR cc_start: 0.8163 (t80) cc_final: 0.7883 (t80) REVERT: J 224 GLN cc_start: 0.7937 (pm20) cc_final: 0.7684 (pm20) REVERT: L 98 MET cc_start: 0.5215 (tpt) cc_final: 0.4814 (tpt) REVERT: L 193 MET cc_start: 0.8520 (mpp) cc_final: 0.8174 (mpp) REVERT: L 206 LEU cc_start: 0.8614 (tp) cc_final: 0.8375 (tp) REVERT: M 67 MET cc_start: 0.7310 (tmm) cc_final: 0.7026 (tmm) REVERT: M 128 GLN cc_start: 0.8087 (mt0) cc_final: 0.7734 (pm20) REVERT: N 168 LYS cc_start: 0.8384 (mmtt) cc_final: 0.7999 (mmtt) REVERT: N 184 GLU cc_start: 0.7367 (tp30) cc_final: 0.6836 (tp30) REVERT: N 185 LYS cc_start: 0.7537 (tppt) cc_final: 0.6828 (tptm) REVERT: N 193 MET cc_start: 0.8563 (mpp) cc_final: 0.7587 (mpp) REVERT: O 98 MET cc_start: 0.8361 (tpp) cc_final: 0.8068 (tpp) REVERT: P 60 ARG cc_start: 0.8429 (ptp-110) cc_final: 0.8076 (ptp-110) REVERT: P 74 SER cc_start: 0.6290 (t) cc_final: 0.6015 (t) REVERT: P 151 MET cc_start: 0.8698 (mtm) cc_final: 0.7947 (mtt) REVERT: P 179 ASP cc_start: 0.7738 (m-30) cc_final: 0.7365 (m-30) REVERT: P 224 GLN cc_start: 0.7307 (pm20) cc_final: 0.7027 (pm20) REVERT: Q 70 MET cc_start: 0.7391 (tpp) cc_final: 0.7007 (ttt) REVERT: Q 167 TYR cc_start: 0.7123 (m-80) cc_final: 0.6841 (m-80) REVERT: R 173 PHE cc_start: 0.7923 (m-10) cc_final: 0.7649 (m-10) REVERT: S 76 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6474 (pttp) REVERT: S 140 PHE cc_start: 0.7460 (p90) cc_final: 0.6574 (p90) REVERT: S 158 PHE cc_start: 0.8545 (m-80) cc_final: 0.8194 (m-10) REVERT: S 192 TYR cc_start: 0.7391 (m-80) cc_final: 0.6831 (m-80) REVERT: T 76 LYS cc_start: 0.7906 (pttp) cc_final: 0.7395 (ptpt) REVERT: U 63 LYS cc_start: 0.6889 (mmtt) cc_final: 0.6191 (mttt) REVERT: U 151 MET cc_start: 0.8043 (mpp) cc_final: 0.7051 (mpp) REVERT: U 160 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7723 (mmmm) REVERT: U 167 TYR cc_start: 0.6408 (m-80) cc_final: 0.6004 (m-80) outliers start: 94 outliers final: 60 residues processed: 1014 average time/residue: 0.5306 time to fit residues: 869.0039 Evaluate side-chains 981 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 918 time to evaluate : 4.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 260 GLN Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 35 SER Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 302 GLN Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 194 ASN Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 89 SER Chi-restraints excluded: chain M residue 170 THR Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 94 SER Chi-restraints excluded: chain P residue 170 THR Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 58 SER Chi-restraints excluded: chain U residue 88 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 424 optimal weight: 20.0000 chunk 322 optimal weight: 7.9990 chunk 222 optimal weight: 0.0370 chunk 47 optimal weight: 4.9990 chunk 204 optimal weight: 0.9990 chunk 288 optimal weight: 7.9990 chunk 430 optimal weight: 0.3980 chunk 456 optimal weight: 10.0000 chunk 225 optimal weight: 1.9990 chunk 408 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 overall best weight: 0.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 318 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 GLN ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 294 ASN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 GLN M 90 GLN N 90 GLN N 198 GLN ** S 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 40492 Z= 0.160 Angle : 0.567 8.636 55039 Z= 0.293 Chirality : 0.040 0.242 6034 Planarity : 0.004 0.056 6770 Dihedral : 14.195 178.986 6276 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.04 % Allowed : 16.08 % Favored : 81.88 % 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: -0.97 (0.12), residues: 4672 helix: 0.66 (0.13), residues: 1753 sheet: -1.24 (0.23), residues: 537 loop : -1.52 (0.12), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 381 HIS 0.004 0.001 HIS U 115 PHE 0.031 0.002 PHE U 140 TYR 0.024 0.001 TYR A 56 ARG 0.006 0.000 ARG B 33 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1068 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 984 time to evaluate : 4.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8875 (tptt) cc_final: 0.8424 (tptp) REVERT: A 187 ASN cc_start: 0.8102 (m-40) cc_final: 0.7832 (t0) REVERT: A 258 MET cc_start: 0.7187 (tpp) cc_final: 0.6900 (tpt) REVERT: A 354 LYS cc_start: 0.7257 (mttt) cc_final: 0.6915 (ttmt) REVERT: B 1 MET cc_start: 0.4191 (mmp) cc_final: 0.3517 (mmp) REVERT: B 33 ARG cc_start: 0.8032 (mtm110) cc_final: 0.7664 (ttt90) REVERT: B 47 SER cc_start: 0.8886 (OUTLIER) cc_final: 0.8581 (t) REVERT: B 154 LYS cc_start: 0.8562 (ttpt) cc_final: 0.8199 (tptp) REVERT: B 158 ASP cc_start: 0.7903 (m-30) cc_final: 0.7240 (m-30) REVERT: B 165 LYS cc_start: 0.8811 (mttm) cc_final: 0.8593 (mttt) REVERT: B 240 MET cc_start: 0.8419 (ttm) cc_final: 0.8002 (ttm) REVERT: B 275 MET cc_start: 0.8678 (tmm) cc_final: 0.8261 (tmm) REVERT: B 297 PHE cc_start: 0.8585 (t80) cc_final: 0.8169 (t80) REVERT: C 394 MET cc_start: 0.6947 (mmm) cc_final: 0.6180 (mpp) REVERT: C 419 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7929 (tm-30) REVERT: D 154 LYS cc_start: 0.8959 (tptm) cc_final: 0.8641 (tppp) REVERT: E 263 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8132 (mt) REVERT: E 297 PHE cc_start: 0.8671 (t80) cc_final: 0.8292 (t80) REVERT: F 1 MET cc_start: 0.5607 (mmm) cc_final: 0.4444 (mmm) REVERT: F 204 MET cc_start: 0.8824 (tpt) cc_final: 0.8579 (tpt) REVERT: F 258 MET cc_start: 0.7915 (mmm) cc_final: 0.7363 (tpp) REVERT: F 377 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7830 (tt0) REVERT: G 63 ASN cc_start: 0.8215 (t0) cc_final: 0.7756 (t0) REVERT: G 236 LYS cc_start: 0.8314 (tttm) cc_final: 0.7934 (tmtt) REVERT: G 394 MET cc_start: 0.7494 (mpp) cc_final: 0.6830 (mmm) REVERT: J 68 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.6019 (mt) REVERT: J 81 TYR cc_start: 0.8137 (t80) cc_final: 0.7928 (t80) REVERT: J 224 GLN cc_start: 0.7972 (pm20) cc_final: 0.7699 (pm20) REVERT: K 95 TYR cc_start: 0.8703 (t80) cc_final: 0.8494 (t80) REVERT: L 190 TRP cc_start: 0.8520 (m100) cc_final: 0.8022 (m100) REVERT: L 193 MET cc_start: 0.8522 (mpp) cc_final: 0.8205 (mpp) REVERT: L 206 LEU cc_start: 0.8497 (tp) cc_final: 0.8267 (tp) REVERT: N 70 MET cc_start: 0.7604 (ttt) cc_final: 0.7386 (tpp) REVERT: N 184 GLU cc_start: 0.7337 (tp30) cc_final: 0.6767 (tp30) REVERT: N 193 MET cc_start: 0.8528 (mpp) cc_final: 0.7638 (mpp) REVERT: O 98 MET cc_start: 0.8202 (tpp) cc_final: 0.7949 (tpp) REVERT: P 60 ARG cc_start: 0.8441 (ptp-110) cc_final: 0.8036 (ptp-110) REVERT: P 179 ASP cc_start: 0.7776 (m-30) cc_final: 0.7402 (m-30) REVERT: P 202 GLN cc_start: 0.8266 (tt0) cc_final: 0.7846 (tm-30) REVERT: P 224 GLN cc_start: 0.7392 (pm20) cc_final: 0.7050 (pm20) REVERT: Q 70 MET cc_start: 0.7377 (tpp) cc_final: 0.6907 (ttt) REVERT: Q 101 LYS cc_start: 0.8178 (mtmt) cc_final: 0.7731 (mtmt) REVERT: Q 167 TYR cc_start: 0.7329 (m-80) cc_final: 0.7052 (m-80) REVERT: S 76 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6337 (pttp) REVERT: S 158 PHE cc_start: 0.8476 (m-80) cc_final: 0.8123 (m-10) REVERT: T 173 PHE cc_start: 0.7772 (m-10) cc_final: 0.7553 (m-10) REVERT: T 192 TYR cc_start: 0.7887 (m-80) cc_final: 0.7572 (m-80) REVERT: U 151 MET cc_start: 0.7817 (mpp) cc_final: 0.6603 (mpp) REVERT: U 167 TYR cc_start: 0.6385 (m-80) cc_final: 0.6073 (m-80) outliers start: 84 outliers final: 52 residues processed: 1025 average time/residue: 0.5238 time to fit residues: 865.5980 Evaluate side-chains 975 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 919 time to evaluate : 4.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 323 GLU Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 89 SER Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain J residue 68 LEU Chi-restraints excluded: chain J residue 194 ASN Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 98 MET Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 217 THR Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain O residue 194 ASN Chi-restraints excluded: chain O residue 221 VAL Chi-restraints excluded: chain P residue 94 SER Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain U residue 119 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 379 optimal weight: 6.9990 chunk 258 optimal weight: 8.9990 chunk 6 optimal weight: 7.9990 chunk 339 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 389 optimal weight: 10.0000 chunk 315 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 232 optimal weight: 30.0000 chunk 409 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 260 GLN A 294 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 GLN G 260 GLN G 294 ASN M 90 GLN M 115 HIS N 90 GLN N 115 HIS ** S 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 40492 Z= 0.383 Angle : 0.666 10.240 55039 Z= 0.344 Chirality : 0.044 0.316 6034 Planarity : 0.005 0.054 6770 Dihedral : 14.238 179.660 6276 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 3.06 % Allowed : 16.54 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.12), residues: 4672 helix: 0.26 (0.13), residues: 1789 sheet: -1.19 (0.21), residues: 624 loop : -1.66 (0.12), residues: 2259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 300 HIS 0.004 0.001 HIS G 203 PHE 0.030 0.002 PHE U 175 TYR 0.024 0.002 TYR T 81 ARG 0.007 0.001 ARG M 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 954 time to evaluate : 4.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8901 (tptt) cc_final: 0.8433 (tptp) REVERT: A 168 ASN cc_start: 0.8347 (t0) cc_final: 0.8070 (t0) REVERT: A 184 VAL cc_start: 0.9258 (OUTLIER) cc_final: 0.8989 (t) REVERT: A 260 GLN cc_start: 0.7466 (OUTLIER) cc_final: 0.7236 (pt0) REVERT: A 334 TYR cc_start: 0.7391 (t80) cc_final: 0.7189 (t80) REVERT: A 354 LYS cc_start: 0.7182 (mttt) cc_final: 0.6551 (mttp) REVERT: B 1 MET cc_start: 0.3961 (mmp) cc_final: 0.3438 (mmp) REVERT: B 47 SER cc_start: 0.8939 (OUTLIER) cc_final: 0.8639 (t) REVERT: B 154 LYS cc_start: 0.8665 (ttpt) cc_final: 0.8282 (tptp) REVERT: B 158 ASP cc_start: 0.8044 (m-30) cc_final: 0.7357 (m-30) REVERT: B 165 LYS cc_start: 0.8781 (mttm) cc_final: 0.8551 (mttt) REVERT: B 240 MET cc_start: 0.8569 (ttm) cc_final: 0.8169 (ttm) REVERT: B 324 TYR cc_start: 0.7556 (m-10) cc_final: 0.7356 (m-10) REVERT: C 192 THR cc_start: 0.8339 (p) cc_final: 0.7957 (p) REVERT: C 263 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8590 (tp) REVERT: C 394 MET cc_start: 0.7037 (mmm) cc_final: 0.6641 (mpp) REVERT: C 419 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7924 (tm-30) REVERT: D 54 TYR cc_start: 0.8571 (m-80) cc_final: 0.8228 (m-80) REVERT: D 143 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.7653 (ttp80) REVERT: D 180 ASP cc_start: 0.7964 (p0) cc_final: 0.7491 (p0) REVERT: D 257 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7525 (tp30) REVERT: E 83 LYS cc_start: 0.9093 (ttpp) cc_final: 0.8777 (ttmm) REVERT: E 253 GLU cc_start: 0.7929 (pm20) cc_final: 0.7602 (pm20) REVERT: F 1 MET cc_start: 0.5402 (mmm) cc_final: 0.4295 (mmm) REVERT: F 204 MET cc_start: 0.8922 (tpt) cc_final: 0.8715 (tpt) REVERT: F 240 MET cc_start: 0.8615 (ttm) cc_final: 0.8295 (ttm) REVERT: F 258 MET cc_start: 0.7926 (mmm) cc_final: 0.7478 (tpt) REVERT: G 119 ASP cc_start: 0.5045 (m-30) cc_final: 0.4713 (m-30) REVERT: G 236 LYS cc_start: 0.8258 (tttm) cc_final: 0.7969 (tmtt) REVERT: G 336 TYR cc_start: 0.7089 (t80) cc_final: 0.6787 (t80) REVERT: G 394 MET cc_start: 0.7434 (mpp) cc_final: 0.6583 (mpp) REVERT: J 81 TYR cc_start: 0.8176 (t80) cc_final: 0.7894 (t80) REVERT: J 138 ARG cc_start: 0.7298 (mmt180) cc_final: 0.6771 (mmm160) REVERT: J 192 TYR cc_start: 0.8104 (m-80) cc_final: 0.7327 (m-80) REVERT: J 224 GLN cc_start: 0.8208 (pm20) cc_final: 0.7991 (pm20) REVERT: K 95 TYR cc_start: 0.8812 (t80) cc_final: 0.8531 (t80) REVERT: L 193 MET cc_start: 0.8675 (mpp) cc_final: 0.8224 (mpp) REVERT: L 206 LEU cc_start: 0.8565 (tp) cc_final: 0.8350 (tp) REVERT: M 81 TYR cc_start: 0.8348 (t80) cc_final: 0.8127 (t80) REVERT: N 70 MET cc_start: 0.7995 (ttt) cc_final: 0.7750 (ttt) REVERT: N 184 GLU cc_start: 0.7396 (tp30) cc_final: 0.6913 (tp30) REVERT: N 185 LYS cc_start: 0.7513 (tppt) cc_final: 0.6749 (tptm) REVERT: N 193 MET cc_start: 0.8610 (mpp) cc_final: 0.7696 (mpp) REVERT: P 60 ARG cc_start: 0.8430 (ptp-110) cc_final: 0.8164 (ptp-110) REVERT: P 151 MET cc_start: 0.8567 (mtm) cc_final: 0.7880 (mtt) REVERT: P 179 ASP cc_start: 0.7818 (m-30) cc_final: 0.7450 (m-30) REVERT: P 224 GLN cc_start: 0.7500 (pm20) cc_final: 0.7178 (pm20) REVERT: Q 98 MET cc_start: 0.7907 (pmm) cc_final: 0.7630 (pmm) REVERT: Q 101 LYS cc_start: 0.7945 (mtmt) cc_final: 0.7621 (mtmt) REVERT: Q 167 TYR cc_start: 0.7370 (m-80) cc_final: 0.7048 (m-80) REVERT: R 156 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7152 (mt-10) REVERT: R 167 TYR cc_start: 0.5938 (m-80) cc_final: 0.5714 (m-80) REVERT: R 176 THR cc_start: 0.7821 (OUTLIER) cc_final: 0.7307 (p) REVERT: S 76 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.6643 (pttp) REVERT: S 192 TYR cc_start: 0.7667 (m-80) cc_final: 0.6900 (m-80) REVERT: T 98 MET cc_start: 0.7728 (mmt) cc_final: 0.7527 (mmm) REVERT: T 173 PHE cc_start: 0.7947 (m-10) cc_final: 0.7718 (m-10) REVERT: T 192 TYR cc_start: 0.7950 (m-80) cc_final: 0.7640 (m-80) REVERT: T 208 PHE cc_start: 0.7855 (OUTLIER) cc_final: 0.7366 (t80) REVERT: U 151 MET cc_start: 0.7874 (mpp) cc_final: 0.6648 (mpp) REVERT: U 160 LYS cc_start: 0.7761 (mmmt) cc_final: 0.7483 (mmmm) REVERT: U 167 TYR cc_start: 0.6609 (m-80) cc_final: 0.6327 (m-80) outliers start: 126 outliers final: 85 residues processed: 1021 average time/residue: 0.5438 time to fit residues: 896.4324 Evaluate side-chains 1015 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 921 time to evaluate : 4.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 412 ILE Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 247 THR Chi-restraints excluded: chain G residue 260 GLN Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain L residue 148 ILE Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 217 THR Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 115 HIS Chi-restraints excluded: chain M residue 170 THR Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 170 THR Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 170 THR Chi-restraints excluded: chain Q residue 88 VAL Chi-restraints excluded: chain R residue 88 VAL Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 58 SER Chi-restraints excluded: chain T residue 207 LYS Chi-restraints excluded: chain T residue 208 PHE Chi-restraints excluded: chain U residue 88 VAL Chi-restraints excluded: chain U residue 119 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 153 optimal weight: 8.9990 chunk 410 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 chunk 267 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 456 optimal weight: 0.4980 chunk 379 optimal weight: 3.9990 chunk 211 optimal weight: 9.9990 chunk 37 optimal weight: 0.0970 chunk 151 optimal weight: 10.0000 chunk 239 optimal weight: 5.9990 overall best weight: 1.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 163 GLN ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 GLN G 251 ASN G 294 ASN M 90 GLN N 90 GLN ** S 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40492 Z= 0.203 Angle : 0.598 8.805 55039 Z= 0.308 Chirality : 0.041 0.279 6034 Planarity : 0.004 0.054 6770 Dihedral : 14.183 179.883 6276 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.77 % Allowed : 17.75 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.12), residues: 4672 helix: 0.53 (0.13), residues: 1760 sheet: -1.12 (0.22), residues: 580 loop : -1.55 (0.12), residues: 2332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 381 HIS 0.019 0.001 HIS M 115 PHE 0.033 0.002 PHE U 140 TYR 0.022 0.001 TYR C 137 ARG 0.008 0.000 ARG O 144 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 961 time to evaluate : 4.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8907 (tptt) cc_final: 0.8437 (tptp) REVERT: A 168 ASN cc_start: 0.8277 (t0) cc_final: 0.7941 (t0) REVERT: A 184 VAL cc_start: 0.9228 (OUTLIER) cc_final: 0.8941 (t) REVERT: A 257 GLU cc_start: 0.7226 (mt-10) cc_final: 0.6981 (tt0) REVERT: A 260 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.7078 (pt0) REVERT: B 1 MET cc_start: 0.3890 (mmp) cc_final: 0.3551 (mmp) REVERT: B 33 ARG cc_start: 0.8056 (mtm110) cc_final: 0.7681 (ttt90) REVERT: B 47 SER cc_start: 0.8955 (OUTLIER) cc_final: 0.8648 (t) REVERT: B 149 MET cc_start: 0.7052 (mtp) cc_final: 0.6780 (mtp) REVERT: B 154 LYS cc_start: 0.8575 (ttpt) cc_final: 0.8205 (tptp) REVERT: B 158 ASP cc_start: 0.8007 (m-30) cc_final: 0.7307 (m-30) REVERT: B 165 LYS cc_start: 0.8567 (mttm) cc_final: 0.8302 (mttt) REVERT: B 170 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7167 (mp-120) REVERT: B 240 MET cc_start: 0.8469 (ttm) cc_final: 0.8060 (ttm) REVERT: B 278 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8288 (pt) REVERT: C 236 LYS cc_start: 0.8322 (ttpp) cc_final: 0.8041 (ttpt) REVERT: C 263 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8564 (tp) REVERT: C 394 MET cc_start: 0.7002 (mmm) cc_final: 0.6218 (mpp) REVERT: C 419 GLU cc_start: 0.8375 (tm-30) cc_final: 0.7717 (tm-30) REVERT: D 54 TYR cc_start: 0.8500 (m-80) cc_final: 0.8210 (m-80) REVERT: D 257 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7413 (tp30) REVERT: E 83 LYS cc_start: 0.9060 (ttpp) cc_final: 0.8775 (ttmm) REVERT: F 1 MET cc_start: 0.5350 (mmm) cc_final: 0.4228 (mmm) REVERT: F 204 MET cc_start: 0.8984 (tpt) cc_final: 0.8782 (tpt) REVERT: F 240 MET cc_start: 0.8547 (ttm) cc_final: 0.8294 (ttm) REVERT: F 258 MET cc_start: 0.7858 (mmm) cc_final: 0.7466 (tpp) REVERT: F 377 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7818 (tt0) REVERT: G 119 ASP cc_start: 0.4890 (m-30) cc_final: 0.4562 (m-30) REVERT: G 236 LYS cc_start: 0.8344 (tttm) cc_final: 0.7956 (tmtt) REVERT: G 336 TYR cc_start: 0.6966 (t80) cc_final: 0.6692 (t80) REVERT: G 394 MET cc_start: 0.7581 (mpp) cc_final: 0.6711 (mpp) REVERT: J 81 TYR cc_start: 0.8033 (t80) cc_final: 0.7787 (t80) REVERT: J 138 ARG cc_start: 0.7114 (mmt180) cc_final: 0.6759 (mmt180) REVERT: J 192 TYR cc_start: 0.7956 (m-80) cc_final: 0.7230 (m-80) REVERT: K 98 MET cc_start: 0.7550 (mtp) cc_final: 0.7334 (mtt) REVERT: L 156 GLU cc_start: 0.7673 (mp0) cc_final: 0.7263 (mp0) REVERT: L 193 MET cc_start: 0.8565 (mpp) cc_final: 0.8188 (mpp) REVERT: L 206 LEU cc_start: 0.8494 (tp) cc_final: 0.8267 (tp) REVERT: N 70 MET cc_start: 0.7850 (ttt) cc_final: 0.7383 (tpp) REVERT: N 184 GLU cc_start: 0.7357 (tp30) cc_final: 0.6867 (tp30) REVERT: N 193 MET cc_start: 0.8736 (mpp) cc_final: 0.8085 (mpp) REVERT: P 151 MET cc_start: 0.8628 (mtm) cc_final: 0.7883 (mtt) REVERT: P 179 ASP cc_start: 0.7901 (m-30) cc_final: 0.7503 (m-30) REVERT: P 202 GLN cc_start: 0.8376 (tt0) cc_final: 0.7872 (tm-30) REVERT: P 224 GLN cc_start: 0.7529 (pm20) cc_final: 0.7186 (pm20) REVERT: Q 101 LYS cc_start: 0.7838 (mtmt) cc_final: 0.7464 (mtmt) REVERT: Q 167 TYR cc_start: 0.7191 (m-80) cc_final: 0.6840 (m-80) REVERT: R 167 TYR cc_start: 0.5860 (m-80) cc_final: 0.5606 (m-80) REVERT: R 173 PHE cc_start: 0.7894 (m-80) cc_final: 0.7414 (t80) REVERT: R 176 THR cc_start: 0.7735 (OUTLIER) cc_final: 0.7266 (p) REVERT: S 76 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6579 (pttp) REVERT: S 192 TYR cc_start: 0.7699 (m-80) cc_final: 0.7021 (m-80) REVERT: T 81 TYR cc_start: 0.7578 (t80) cc_final: 0.7263 (t80) REVERT: T 98 MET cc_start: 0.7626 (mmt) cc_final: 0.7415 (mmm) REVERT: T 115 HIS cc_start: 0.7161 (m90) cc_final: 0.6955 (m90) REVERT: T 173 PHE cc_start: 0.7813 (m-10) cc_final: 0.7459 (m-10) REVERT: T 192 TYR cc_start: 0.7881 (m-80) cc_final: 0.7623 (m-80) REVERT: T 208 PHE cc_start: 0.7831 (OUTLIER) cc_final: 0.7439 (t80) REVERT: U 63 LYS cc_start: 0.7189 (mmtt) cc_final: 0.6122 (mmmt) REVERT: U 151 MET cc_start: 0.7771 (mpp) cc_final: 0.6521 (mpp) REVERT: U 160 LYS cc_start: 0.7720 (mmmt) cc_final: 0.7419 (mmmm) REVERT: U 167 TYR cc_start: 0.6595 (m-80) cc_final: 0.6304 (m-80) outliers start: 114 outliers final: 77 residues processed: 1022 average time/residue: 0.5106 time to fit residues: 841.9480 Evaluate side-chains 1007 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 920 time to evaluate : 4.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 8 ILE Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 284 SER Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 135 LEU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 170 THR Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 170 THR Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 107 ILE Chi-restraints excluded: chain S residue 155 SER Chi-restraints excluded: chain T residue 208 PHE Chi-restraints excluded: chain T residue 211 ILE Chi-restraints excluded: chain U residue 119 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 440 optimal weight: 40.0000 chunk 51 optimal weight: 20.0000 chunk 260 optimal weight: 2.9990 chunk 333 optimal weight: 1.9990 chunk 258 optimal weight: 6.9990 chunk 384 optimal weight: 3.9990 chunk 255 optimal weight: 10.0000 chunk 454 optimal weight: 0.5980 chunk 284 optimal weight: 0.9990 chunk 277 optimal weight: 10.0000 chunk 210 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 ASN A 148 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 GLN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 GLN M 90 GLN N 90 GLN ** S 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 90 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 40492 Z= 0.214 Angle : 0.596 8.127 55039 Z= 0.306 Chirality : 0.041 0.262 6034 Planarity : 0.004 0.053 6770 Dihedral : 14.151 179.391 6276 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 2.82 % Allowed : 18.16 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.12), residues: 4672 helix: 0.58 (0.13), residues: 1765 sheet: -1.07 (0.22), residues: 590 loop : -1.52 (0.12), residues: 2317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 381 HIS 0.002 0.001 HIS L 115 PHE 0.037 0.002 PHE U 140 TYR 0.018 0.001 TYR A 56 ARG 0.007 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 945 time to evaluate : 4.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8897 (tptt) cc_final: 0.8406 (tptp) REVERT: A 168 ASN cc_start: 0.8403 (t0) cc_final: 0.8151 (t0) REVERT: A 184 VAL cc_start: 0.9217 (OUTLIER) cc_final: 0.8917 (t) REVERT: A 258 MET cc_start: 0.7205 (tpp) cc_final: 0.6778 (tpp) REVERT: A 324 TYR cc_start: 0.7931 (m-10) cc_final: 0.7684 (m-10) REVERT: B 33 ARG cc_start: 0.8104 (mtm110) cc_final: 0.7718 (ttt90) REVERT: B 47 SER cc_start: 0.8940 (OUTLIER) cc_final: 0.8636 (t) REVERT: B 149 MET cc_start: 0.7072 (mtp) cc_final: 0.6807 (mtp) REVERT: B 154 LYS cc_start: 0.8571 (ttpt) cc_final: 0.8196 (tptp) REVERT: B 158 ASP cc_start: 0.7957 (m-30) cc_final: 0.7230 (m-30) REVERT: B 165 LYS cc_start: 0.8520 (mttm) cc_final: 0.8247 (mttt) REVERT: B 170 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7057 (mp-120) REVERT: B 240 MET cc_start: 0.8456 (ttm) cc_final: 0.8250 (ttm) REVERT: B 278 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8261 (pt) REVERT: C 187 ASN cc_start: 0.8804 (t0) cc_final: 0.8347 (t0) REVERT: C 236 LYS cc_start: 0.8325 (ttpp) cc_final: 0.8043 (ttpt) REVERT: C 394 MET cc_start: 0.6989 (mmm) cc_final: 0.6211 (mpp) REVERT: C 419 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7717 (tm-30) REVERT: D 54 TYR cc_start: 0.8479 (m-80) cc_final: 0.8142 (m-80) REVERT: D 257 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7417 (tp30) REVERT: D 411 THR cc_start: 0.8309 (p) cc_final: 0.8026 (p) REVERT: E 83 LYS cc_start: 0.9060 (ttpp) cc_final: 0.8766 (ttmm) REVERT: F 1 MET cc_start: 0.5335 (mmm) cc_final: 0.4258 (mmm) REVERT: F 63 ASN cc_start: 0.7843 (t0) cc_final: 0.7318 (t0) REVERT: F 151 GLU cc_start: 0.7968 (tp30) cc_final: 0.7759 (tp30) REVERT: F 258 MET cc_start: 0.7883 (mmm) cc_final: 0.7475 (tpp) REVERT: F 327 LEU cc_start: 0.9118 (mt) cc_final: 0.8895 (mp) REVERT: F 377 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7815 (tt0) REVERT: G 119 ASP cc_start: 0.4883 (m-30) cc_final: 0.4550 (m-30) REVERT: G 236 LYS cc_start: 0.8363 (tttm) cc_final: 0.7955 (tmtt) REVERT: G 336 TYR cc_start: 0.7006 (t80) cc_final: 0.6654 (t80) REVERT: G 394 MET cc_start: 0.7582 (mpp) cc_final: 0.6714 (mpp) REVERT: J 81 TYR cc_start: 0.8012 (t80) cc_final: 0.7741 (t80) REVERT: J 138 ARG cc_start: 0.7065 (mmt180) cc_final: 0.6587 (mmt-90) REVERT: J 192 TYR cc_start: 0.7979 (m-80) cc_final: 0.7244 (m-80) REVERT: L 156 GLU cc_start: 0.7769 (mp0) cc_final: 0.7356 (mp0) REVERT: L 193 MET cc_start: 0.8573 (mpp) cc_final: 0.8172 (mpp) REVERT: M 81 TYR cc_start: 0.8223 (t80) cc_final: 0.7988 (t80) REVERT: N 184 GLU cc_start: 0.7361 (tp30) cc_final: 0.6863 (tp30) REVERT: N 193 MET cc_start: 0.8701 (mpp) cc_final: 0.8090 (mpp) REVERT: P 179 ASP cc_start: 0.7889 (m-30) cc_final: 0.7507 (m-30) REVERT: P 202 GLN cc_start: 0.8369 (tt0) cc_final: 0.7861 (tm-30) REVERT: P 224 GLN cc_start: 0.7526 (pm20) cc_final: 0.7206 (pm20) REVERT: Q 101 LYS cc_start: 0.7794 (mtmt) cc_final: 0.7499 (mtmt) REVERT: Q 167 TYR cc_start: 0.7174 (m-80) cc_final: 0.6818 (m-80) REVERT: R 173 PHE cc_start: 0.7888 (m-80) cc_final: 0.7520 (t80) REVERT: R 176 THR cc_start: 0.7692 (OUTLIER) cc_final: 0.7217 (p) REVERT: S 76 LYS cc_start: 0.7147 (OUTLIER) cc_final: 0.6571 (pttp) REVERT: S 192 TYR cc_start: 0.7812 (m-80) cc_final: 0.7190 (m-80) REVERT: T 173 PHE cc_start: 0.7795 (m-10) cc_final: 0.7472 (m-10) REVERT: T 192 TYR cc_start: 0.7874 (m-80) cc_final: 0.7614 (m-80) REVERT: T 208 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.7310 (t80) REVERT: U 63 LYS cc_start: 0.7033 (mmtt) cc_final: 0.5960 (mmmt) REVERT: U 151 MET cc_start: 0.7762 (mpp) cc_final: 0.6498 (mpp) REVERT: U 160 LYS cc_start: 0.7771 (mmmt) cc_final: 0.7469 (mmmm) REVERT: U 167 TYR cc_start: 0.6580 (m-80) cc_final: 0.6279 (m-80) outliers start: 116 outliers final: 89 residues processed: 1008 average time/residue: 0.5156 time to fit residues: 835.4986 Evaluate side-chains 1024 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 927 time to evaluate : 4.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 116 VAL Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 121 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 347 GLN Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 311 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 217 THR Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain N residue 134 THR Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 170 THR Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 194 ASN Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 155 SER Chi-restraints excluded: chain P residue 170 THR Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 107 ILE Chi-restraints excluded: chain S residue 155 SER Chi-restraints excluded: chain T residue 208 PHE Chi-restraints excluded: chain T residue 211 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 281 optimal weight: 10.0000 chunk 181 optimal weight: 7.9990 chunk 271 optimal weight: 9.9990 chunk 137 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 289 optimal weight: 20.0000 chunk 309 optimal weight: 9.9990 chunk 224 optimal weight: 7.9990 chunk 42 optimal weight: 10.0000 chunk 357 optimal weight: 0.5980 overall best weight: 5.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN C 294 ASN ** D 260 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 260 GLN E 294 ASN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 260 GLN G 294 ASN M 90 GLN M 115 HIS N 90 GLN ** S 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 40492 Z= 0.379 Angle : 0.677 10.331 55039 Z= 0.349 Chirality : 0.044 0.311 6034 Planarity : 0.005 0.053 6770 Dihedral : 14.226 179.894 6276 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 3.21 % Allowed : 18.21 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.12), residues: 4672 helix: 0.27 (0.13), residues: 1780 sheet: -1.11 (0.21), residues: 636 loop : -1.65 (0.12), residues: 2256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP O 91 HIS 0.004 0.001 HIS N 188 PHE 0.036 0.002 PHE U 140 TYR 0.027 0.002 TYR T 81 ARG 0.009 0.001 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 943 time to evaluate : 4.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8866 (tptt) cc_final: 0.8369 (tptp) REVERT: A 168 ASN cc_start: 0.8515 (t0) cc_final: 0.8243 (t0) REVERT: A 184 VAL cc_start: 0.9284 (OUTLIER) cc_final: 0.8973 (t) REVERT: A 253 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6637 (pm20) REVERT: A 324 TYR cc_start: 0.7997 (m-10) cc_final: 0.7749 (m-10) REVERT: A 354 LYS cc_start: 0.7110 (mttt) cc_final: 0.6515 (mttp) REVERT: B 47 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8682 (t) REVERT: B 154 LYS cc_start: 0.8677 (ttpt) cc_final: 0.8334 (tptp) REVERT: B 158 ASP cc_start: 0.7994 (m-30) cc_final: 0.7483 (m-30) REVERT: B 165 LYS cc_start: 0.8540 (mttm) cc_final: 0.8260 (mttt) REVERT: B 170 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7219 (mp-120) REVERT: B 240 MET cc_start: 0.8568 (ttm) cc_final: 0.8332 (ttm) REVERT: C 89 SER cc_start: 0.9139 (m) cc_final: 0.8727 (p) REVERT: C 192 THR cc_start: 0.8354 (p) cc_final: 0.7964 (p) REVERT: C 236 LYS cc_start: 0.8417 (ttpp) cc_final: 0.8102 (ttpt) REVERT: C 263 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8546 (tp) REVERT: C 394 MET cc_start: 0.7069 (mmm) cc_final: 0.6682 (mpp) REVERT: C 419 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8005 (tm-30) REVERT: D 34 LYS cc_start: 0.5021 (mtpt) cc_final: 0.4623 (mtpt) REVERT: D 54 TYR cc_start: 0.8638 (m-80) cc_final: 0.8196 (m-80) REVERT: D 143 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.7659 (ttp80) REVERT: D 180 ASP cc_start: 0.7778 (p0) cc_final: 0.7425 (p0) REVERT: D 183 ASP cc_start: 0.8562 (t0) cc_final: 0.8336 (t0) REVERT: D 257 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7420 (tp30) REVERT: D 411 THR cc_start: 0.8405 (p) cc_final: 0.8147 (p) REVERT: E 83 LYS cc_start: 0.9137 (ttpp) cc_final: 0.8860 (ttmm) REVERT: F 1 MET cc_start: 0.5384 (mmm) cc_final: 0.4423 (mmm) REVERT: F 63 ASN cc_start: 0.7967 (t0) cc_final: 0.7458 (t0) REVERT: F 244 ASP cc_start: 0.8172 (t0) cc_final: 0.7961 (t0) REVERT: F 327 LEU cc_start: 0.9138 (mt) cc_final: 0.8898 (mp) REVERT: G 119 ASP cc_start: 0.5133 (m-30) cc_final: 0.4824 (m-30) REVERT: G 336 TYR cc_start: 0.7097 (t80) cc_final: 0.6769 (t80) REVERT: G 394 MET cc_start: 0.7451 (mpp) cc_final: 0.6722 (mpp) REVERT: J 81 TYR cc_start: 0.8111 (t80) cc_final: 0.7817 (t80) REVERT: J 138 ARG cc_start: 0.7417 (mmt180) cc_final: 0.6899 (mmm160) REVERT: J 192 TYR cc_start: 0.8178 (m-80) cc_final: 0.7818 (m-10) REVERT: L 62 GLU cc_start: 0.7481 (tp30) cc_final: 0.7212 (tp30) REVERT: L 193 MET cc_start: 0.8723 (mpp) cc_final: 0.8198 (mpp) REVERT: M 81 TYR cc_start: 0.8316 (t80) cc_final: 0.8116 (t80) REVERT: N 184 GLU cc_start: 0.7352 (tp30) cc_final: 0.6908 (tp30) REVERT: N 193 MET cc_start: 0.8721 (mpp) cc_final: 0.8219 (mtm) REVERT: O 91 TRP cc_start: 0.8661 (p-90) cc_final: 0.8428 (p-90) REVERT: O 98 MET cc_start: 0.8361 (tpp) cc_final: 0.8161 (tpp) REVERT: P 151 MET cc_start: 0.8514 (mtt) cc_final: 0.7737 (mtt) REVERT: P 179 ASP cc_start: 0.7918 (m-30) cc_final: 0.7561 (m-30) REVERT: Q 101 LYS cc_start: 0.7861 (mtmt) cc_final: 0.7510 (mtmt) REVERT: Q 167 TYR cc_start: 0.6979 (m-80) cc_final: 0.6587 (m-80) REVERT: R 156 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7267 (mt-10) REVERT: R 173 PHE cc_start: 0.8041 (m-80) cc_final: 0.7717 (t80) REVERT: S 140 PHE cc_start: 0.6409 (p90) cc_final: 0.5843 (p90) REVERT: S 193 MET cc_start: 0.5475 (mmt) cc_final: 0.5116 (mmt) REVERT: T 173 PHE cc_start: 0.7963 (m-10) cc_final: 0.7589 (m-10) REVERT: T 192 TYR cc_start: 0.7955 (m-80) cc_final: 0.7688 (m-80) REVERT: T 207 LYS cc_start: 0.7508 (pptt) cc_final: 0.7266 (pptt) REVERT: T 208 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7163 (t80) REVERT: U 63 LYS cc_start: 0.7115 (mmtt) cc_final: 0.6058 (mmmt) REVERT: U 151 MET cc_start: 0.7883 (mpp) cc_final: 0.6785 (mpp) REVERT: U 167 TYR cc_start: 0.6608 (m-80) cc_final: 0.6294 (m-80) outliers start: 132 outliers final: 101 residues processed: 1012 average time/residue: 0.5250 time to fit residues: 854.9634 Evaluate side-chains 1030 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 921 time to evaluate : 4.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 158 ASP Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 260 GLN Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain E residue 260 GLN Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 164 CYS Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain G residue 107 LEU Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 260 GLN Chi-restraints excluded: chain G residue 332 LEU Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 217 THR Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain N residue 68 LEU Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 170 THR Chi-restraints excluded: chain N residue 171 LEU Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain P residue 74 SER Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 170 THR Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 107 ILE Chi-restraints excluded: chain S residue 155 SER Chi-restraints excluded: chain T residue 58 SER Chi-restraints excluded: chain T residue 208 PHE Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain U residue 152 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 413 optimal weight: 20.0000 chunk 435 optimal weight: 9.9990 chunk 397 optimal weight: 9.9990 chunk 423 optimal weight: 0.5980 chunk 255 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 332 optimal weight: 4.9990 chunk 130 optimal weight: 0.5980 chunk 383 optimal weight: 30.0000 chunk 400 optimal weight: 7.9990 chunk 422 optimal weight: 40.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 148 GLN A 260 GLN A 294 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 ASN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 294 ASN D 187 ASN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 294 ASN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 347 GLN G 294 ASN M 90 GLN O 90 GLN ** S 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 40492 Z= 0.239 Angle : 0.626 10.033 55039 Z= 0.322 Chirality : 0.042 0.277 6034 Planarity : 0.004 0.053 6770 Dihedral : 14.193 179.932 6276 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 3.01 % Allowed : 18.72 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.12), residues: 4672 helix: 0.49 (0.13), residues: 1753 sheet: -1.08 (0.22), residues: 593 loop : -1.54 (0.12), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP G 300 HIS 0.003 0.001 HIS L 115 PHE 0.035 0.002 PHE U 140 TYR 0.025 0.001 TYR C 137 ARG 0.008 0.000 ARG A 399 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 937 time to evaluate : 4.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8889 (tptt) cc_final: 0.8390 (tptp) REVERT: A 168 ASN cc_start: 0.8465 (t0) cc_final: 0.8203 (t0) REVERT: A 184 VAL cc_start: 0.9245 (OUTLIER) cc_final: 0.8911 (t) REVERT: A 253 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.6773 (pm20) REVERT: A 258 MET cc_start: 0.7117 (tpp) cc_final: 0.6630 (tpp) REVERT: A 260 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6953 (pt0) REVERT: A 324 TYR cc_start: 0.7978 (m-10) cc_final: 0.7741 (m-10) REVERT: B 33 ARG cc_start: 0.8028 (mtm110) cc_final: 0.7621 (ttt90) REVERT: B 47 SER cc_start: 0.8961 (OUTLIER) cc_final: 0.8676 (t) REVERT: B 154 LYS cc_start: 0.8647 (ttpt) cc_final: 0.8249 (tptp) REVERT: B 158 ASP cc_start: 0.7949 (m-30) cc_final: 0.7239 (m-30) REVERT: B 165 LYS cc_start: 0.8508 (mttm) cc_final: 0.8252 (mttt) REVERT: B 170 GLN cc_start: 0.8163 (OUTLIER) cc_final: 0.7085 (mp-120) REVERT: B 240 MET cc_start: 0.8514 (ttm) cc_final: 0.8297 (ttm) REVERT: B 278 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8314 (pt) REVERT: B 388 LYS cc_start: 0.8432 (ptpp) cc_final: 0.8000 (ptpp) REVERT: C 187 ASN cc_start: 0.8850 (t0) cc_final: 0.8486 (t0) REVERT: C 263 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8470 (tp) REVERT: C 394 MET cc_start: 0.7062 (mmm) cc_final: 0.6629 (mpp) REVERT: D 54 TYR cc_start: 0.8640 (m-80) cc_final: 0.8262 (m-80) REVERT: D 257 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7367 (tp30) REVERT: D 411 THR cc_start: 0.8411 (p) cc_final: 0.8131 (p) REVERT: E 83 LYS cc_start: 0.9111 (ttpp) cc_final: 0.8827 (ttmm) REVERT: F 1 MET cc_start: 0.5350 (mmm) cc_final: 0.4285 (mmm) REVERT: F 63 ASN cc_start: 0.7926 (t0) cc_final: 0.7436 (t0) REVERT: F 258 MET cc_start: 0.7857 (mmm) cc_final: 0.7617 (tpp) REVERT: F 327 LEU cc_start: 0.9141 (mt) cc_final: 0.8911 (mp) REVERT: F 402 MET cc_start: 0.8260 (ptm) cc_final: 0.7981 (ptp) REVERT: G 119 ASP cc_start: 0.5074 (m-30) cc_final: 0.4763 (m-30) REVERT: G 200 MET cc_start: 0.8344 (ttp) cc_final: 0.8096 (ttp) REVERT: G 336 TYR cc_start: 0.6994 (t80) cc_final: 0.6678 (t80) REVERT: G 394 MET cc_start: 0.7451 (mpp) cc_final: 0.6677 (mpp) REVERT: J 81 TYR cc_start: 0.7993 (t80) cc_final: 0.7777 (t80) REVERT: J 138 ARG cc_start: 0.7313 (mmt180) cc_final: 0.6741 (mmm160) REVERT: J 192 TYR cc_start: 0.8083 (m-80) cc_final: 0.7769 (m-80) REVERT: L 193 MET cc_start: 0.8650 (mpp) cc_final: 0.8209 (mpp) REVERT: M 81 TYR cc_start: 0.8221 (t80) cc_final: 0.7994 (t80) REVERT: N 184 GLU cc_start: 0.7344 (tp30) cc_final: 0.6908 (tp30) REVERT: N 193 MET cc_start: 0.8633 (mpp) cc_final: 0.8131 (mtm) REVERT: O 98 MET cc_start: 0.8235 (tpp) cc_final: 0.7971 (tpp) REVERT: P 151 MET cc_start: 0.8555 (mtt) cc_final: 0.7677 (mtt) REVERT: P 179 ASP cc_start: 0.7880 (m-30) cc_final: 0.7477 (m-30) REVERT: Q 101 LYS cc_start: 0.7757 (mtmt) cc_final: 0.7437 (mtmt) REVERT: Q 167 TYR cc_start: 0.6961 (m-80) cc_final: 0.6561 (m-80) REVERT: Q 173 PHE cc_start: 0.8018 (m-80) cc_final: 0.7574 (t80) REVERT: R 156 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7335 (mt-10) REVERT: R 173 PHE cc_start: 0.8002 (m-80) cc_final: 0.7598 (t80) REVERT: R 193 MET cc_start: 0.6109 (mmt) cc_final: 0.4271 (tpt) REVERT: S 140 PHE cc_start: 0.6399 (p90) cc_final: 0.5822 (p90) REVERT: T 173 PHE cc_start: 0.7800 (m-10) cc_final: 0.7478 (m-10) REVERT: T 192 TYR cc_start: 0.7933 (m-80) cc_final: 0.7678 (m-80) REVERT: T 207 LYS cc_start: 0.7487 (pptt) cc_final: 0.7255 (pptt) REVERT: T 208 PHE cc_start: 0.8024 (OUTLIER) cc_final: 0.7042 (t80) REVERT: U 63 LYS cc_start: 0.7106 (mmtt) cc_final: 0.6043 (mmmt) REVERT: U 151 MET cc_start: 0.7829 (mpp) cc_final: 0.6743 (mpp) REVERT: U 160 LYS cc_start: 0.7735 (mmmt) cc_final: 0.7424 (mmmm) REVERT: U 167 TYR cc_start: 0.6596 (m-80) cc_final: 0.6270 (m-80) outliers start: 124 outliers final: 101 residues processed: 1004 average time/residue: 0.5286 time to fit residues: 854.4197 Evaluate side-chains 1029 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 919 time to evaluate : 4.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 260 GLN Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 187 ASN Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain D residue 402 MET Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 106 LYS Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 217 THR Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 170 THR Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 203 LYS Chi-restraints excluded: chain P residue 74 SER Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 170 THR Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 107 ILE Chi-restraints excluded: chain S residue 155 SER Chi-restraints excluded: chain T residue 58 SER Chi-restraints excluded: chain T residue 208 PHE Chi-restraints excluded: chain U residue 119 THR Chi-restraints excluded: chain U residue 152 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 278 optimal weight: 9.9990 chunk 448 optimal weight: 20.0000 chunk 273 optimal weight: 4.9990 chunk 212 optimal weight: 0.9980 chunk 311 optimal weight: 7.9990 chunk 470 optimal weight: 6.9990 chunk 432 optimal weight: 0.0470 chunk 374 optimal weight: 8.9990 chunk 38 optimal weight: 20.0000 chunk 289 optimal weight: 9.9990 chunk 229 optimal weight: 0.9980 overall best weight: 2.8082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN N 90 GLN ** S 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 40492 Z= 0.256 Angle : 0.638 14.563 55039 Z= 0.327 Chirality : 0.042 0.274 6034 Planarity : 0.005 0.088 6770 Dihedral : 14.190 179.616 6276 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.84 % Allowed : 19.14 % Favored : 78.02 % 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: -1.09 (0.12), residues: 4672 helix: 0.44 (0.13), residues: 1765 sheet: -1.06 (0.22), residues: 597 loop : -1.55 (0.12), residues: 2310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.001 TRP G 300 HIS 0.003 0.001 HIS N 188 PHE 0.042 0.002 PHE D 171 TYR 0.034 0.001 TYR C 137 ARG 0.013 0.001 ARG F 7 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9344 Ramachandran restraints generated. 4672 Oldfield, 0 Emsley, 4672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 924 time to evaluate : 4.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 LYS cc_start: 0.8878 (tptt) cc_final: 0.8384 (tptp) REVERT: A 168 ASN cc_start: 0.8471 (t0) cc_final: 0.8211 (t0) REVERT: A 184 VAL cc_start: 0.9243 (OUTLIER) cc_final: 0.8913 (t) REVERT: A 253 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.6827 (pm20) REVERT: A 258 MET cc_start: 0.7191 (tpp) cc_final: 0.6709 (tpp) REVERT: A 324 TYR cc_start: 0.7978 (m-10) cc_final: 0.7738 (m-10) REVERT: B 33 ARG cc_start: 0.8050 (mtm110) cc_final: 0.7619 (ttt90) REVERT: B 47 SER cc_start: 0.8964 (OUTLIER) cc_final: 0.8678 (t) REVERT: B 154 LYS cc_start: 0.8643 (ttpt) cc_final: 0.8252 (tptp) REVERT: B 158 ASP cc_start: 0.7951 (m-30) cc_final: 0.7246 (m-30) REVERT: B 165 LYS cc_start: 0.8510 (mttm) cc_final: 0.8237 (mttt) REVERT: B 170 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7103 (mp-120) REVERT: B 240 MET cc_start: 0.8514 (ttm) cc_final: 0.8296 (ttm) REVERT: B 278 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8310 (pt) REVERT: B 388 LYS cc_start: 0.8439 (ptpp) cc_final: 0.8007 (ptpp) REVERT: C 187 ASN cc_start: 0.8854 (t0) cc_final: 0.8491 (t0) REVERT: C 263 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8464 (tp) REVERT: C 394 MET cc_start: 0.7056 (mmm) cc_final: 0.6610 (mpp) REVERT: D 54 TYR cc_start: 0.8650 (m-80) cc_final: 0.8291 (m-80) REVERT: D 143 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.7594 (ttp80) REVERT: D 257 GLU cc_start: 0.7853 (OUTLIER) cc_final: 0.7379 (tp30) REVERT: D 354 LYS cc_start: 0.7510 (mtpt) cc_final: 0.7262 (ptpt) REVERT: D 411 THR cc_start: 0.8411 (p) cc_final: 0.8127 (p) REVERT: E 83 LYS cc_start: 0.9115 (ttpp) cc_final: 0.8820 (ttmm) REVERT: F 1 MET cc_start: 0.5366 (mmm) cc_final: 0.4365 (mmm) REVERT: F 63 ASN cc_start: 0.7936 (t0) cc_final: 0.7448 (t0) REVERT: G 119 ASP cc_start: 0.5079 (m-30) cc_final: 0.4773 (m-30) REVERT: G 200 MET cc_start: 0.8324 (ttp) cc_final: 0.8091 (ttp) REVERT: G 336 TYR cc_start: 0.6993 (t80) cc_final: 0.6681 (t80) REVERT: G 394 MET cc_start: 0.7459 (mpp) cc_final: 0.6682 (mpp) REVERT: J 81 TYR cc_start: 0.8005 (t80) cc_final: 0.7785 (t80) REVERT: J 138 ARG cc_start: 0.7316 (mmt180) cc_final: 0.6740 (mmm160) REVERT: J 192 TYR cc_start: 0.8095 (m-80) cc_final: 0.7772 (m-80) REVERT: L 62 GLU cc_start: 0.7597 (tp30) cc_final: 0.7298 (tp30) REVERT: L 193 MET cc_start: 0.8659 (mpp) cc_final: 0.8201 (mpp) REVERT: N 184 GLU cc_start: 0.7343 (tp30) cc_final: 0.6906 (tp30) REVERT: N 193 MET cc_start: 0.8627 (mpp) cc_final: 0.8154 (mtm) REVERT: O 91 TRP cc_start: 0.8597 (p-90) cc_final: 0.8361 (p-90) REVERT: O 98 MET cc_start: 0.8315 (tpp) cc_final: 0.8040 (tpp) REVERT: O 194 ASN cc_start: 0.8385 (p0) cc_final: 0.8015 (p0) REVERT: P 151 MET cc_start: 0.8548 (mtt) cc_final: 0.7760 (mtm) REVERT: P 179 ASP cc_start: 0.7881 (m-30) cc_final: 0.7532 (m-30) REVERT: P 202 GLN cc_start: 0.8402 (tt0) cc_final: 0.7832 (tm-30) REVERT: Q 101 LYS cc_start: 0.7755 (mtmt) cc_final: 0.7434 (mtmt) REVERT: Q 167 TYR cc_start: 0.6945 (m-80) cc_final: 0.6551 (m-80) REVERT: Q 173 PHE cc_start: 0.7996 (m-80) cc_final: 0.7539 (t80) REVERT: R 156 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7354 (mt-10) REVERT: R 173 PHE cc_start: 0.8021 (m-80) cc_final: 0.7583 (t80) REVERT: R 193 MET cc_start: 0.6118 (mmt) cc_final: 0.4278 (tpt) REVERT: S 140 PHE cc_start: 0.6396 (p90) cc_final: 0.5837 (p90) REVERT: T 173 PHE cc_start: 0.7807 (m-10) cc_final: 0.7480 (m-10) REVERT: T 192 TYR cc_start: 0.7944 (m-80) cc_final: 0.7690 (m-80) REVERT: T 207 LYS cc_start: 0.7357 (pptt) cc_final: 0.7151 (pptt) REVERT: T 208 PHE cc_start: 0.8015 (OUTLIER) cc_final: 0.7131 (t80) REVERT: U 63 LYS cc_start: 0.7107 (mmtt) cc_final: 0.6044 (mmmt) REVERT: U 151 MET cc_start: 0.7830 (mpp) cc_final: 0.6737 (mpp) REVERT: U 160 LYS cc_start: 0.7727 (mmmt) cc_final: 0.7417 (mmmm) REVERT: U 167 TYR cc_start: 0.6603 (m-80) cc_final: 0.6269 (m-80) outliers start: 117 outliers final: 99 residues processed: 987 average time/residue: 0.5185 time to fit residues: 823.5840 Evaluate side-chains 1025 residues out of total 4172 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 917 time to evaluate : 4.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 212 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 253 GLU Chi-restraints excluded: chain A residue 256 ASP Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 356 THR Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 170 GLN Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 249 ILE Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 379 LEU Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 219 VAL Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 326 SER Chi-restraints excluded: chain C residue 409 GLU Chi-restraints excluded: chain D residue 64 VAL Chi-restraints excluded: chain D residue 89 SER Chi-restraints excluded: chain D residue 143 ARG Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 230 THR Chi-restraints excluded: chain D residue 241 SER Chi-restraints excluded: chain D residue 242 THR Chi-restraints excluded: chain D residue 257 GLU Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain D residue 314 ARG Chi-restraints excluded: chain D residue 328 THR Chi-restraints excluded: chain D residue 376 VAL Chi-restraints excluded: chain E residue 8 ILE Chi-restraints excluded: chain E residue 89 SER Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 149 MET Chi-restraints excluded: chain E residue 243 GLU Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain E residue 418 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 10 ASP Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 125 SER Chi-restraints excluded: chain F residue 169 GLU Chi-restraints excluded: chain F residue 181 ILE Chi-restraints excluded: chain F residue 184 VAL Chi-restraints excluded: chain F residue 219 VAL Chi-restraints excluded: chain F residue 230 THR Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 376 VAL Chi-restraints excluded: chain F residue 409 GLU Chi-restraints excluded: chain G residue 86 LYS Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 230 THR Chi-restraints excluded: chain G residue 376 VAL Chi-restraints excluded: chain G residue 379 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 123 LEU Chi-restraints excluded: chain J residue 130 GLU Chi-restraints excluded: chain J residue 152 PHE Chi-restraints excluded: chain J residue 212 LEU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 148 ILE Chi-restraints excluded: chain K residue 219 THR Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 99 VAL Chi-restraints excluded: chain L residue 183 ASN Chi-restraints excluded: chain L residue 217 THR Chi-restraints excluded: chain L residue 221 VAL Chi-restraints excluded: chain M residue 74 SER Chi-restraints excluded: chain M residue 80 SER Chi-restraints excluded: chain M residue 217 THR Chi-restraints excluded: chain M residue 223 ASP Chi-restraints excluded: chain N residue 148 ILE Chi-restraints excluded: chain N residue 170 THR Chi-restraints excluded: chain N residue 213 SER Chi-restraints excluded: chain O residue 55 ASP Chi-restraints excluded: chain O residue 59 LEU Chi-restraints excluded: chain O residue 82 ASP Chi-restraints excluded: chain O residue 141 LEU Chi-restraints excluded: chain O residue 170 THR Chi-restraints excluded: chain O residue 203 LYS Chi-restraints excluded: chain P residue 74 SER Chi-restraints excluded: chain P residue 89 SER Chi-restraints excluded: chain P residue 170 THR Chi-restraints excluded: chain R residue 93 ASN Chi-restraints excluded: chain R residue 176 THR Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 59 LEU Chi-restraints excluded: chain S residue 76 LYS Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 107 ILE Chi-restraints excluded: chain S residue 155 SER Chi-restraints excluded: chain T residue 58 SER Chi-restraints excluded: chain T residue 208 PHE Chi-restraints excluded: chain U residue 119 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 472 random chunks: chunk 297 optimal weight: 0.0050 chunk 398 optimal weight: 0.1980 chunk 114 optimal weight: 10.0000 chunk 345 optimal weight: 1.9990 chunk 55 optimal weight: 0.2980 chunk 104 optimal weight: 0.0770 chunk 375 optimal weight: 0.6980 chunk 156 optimal weight: 0.0570 chunk 385 optimal weight: 0.0050 chunk 47 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.0684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 294 ASN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 ASN ** B 302 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN C 294 ASN C 302 GLN ** D 233 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 ASN D 294 ASN ** F 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 233 HIS ** F 347 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 90 GLN N 90 GLN N 115 HIS ** P 198 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.193007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.156401 restraints weight = 51243.423| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 2.86 r_work: 0.3678 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 40492 Z= 0.162 Angle : 0.610 10.035 55039 Z= 0.312 Chirality : 0.040 0.194 6034 Planarity : 0.004 0.054 6770 Dihedral : 14.099 177.886 6276 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.99 % Allowed : 20.01 % Favored : 78.00 % 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: -0.81 (0.12), residues: 4672 helix: 0.71 (0.13), residues: 1735 sheet: -0.91 (0.23), residues: 553 loop : -1.40 (0.12), residues: 2384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.001 TRP G 300 HIS 0.003 0.001 HIS D 233 PHE 0.037 0.002 PHE U 140 TYR 0.028 0.001 TYR C 137 ARG 0.010 0.001 ARG F 7 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12651.20 seconds wall clock time: 230 minutes 8.31 seconds (13808.31 seconds total)