Starting phenix.real_space_refine on Wed Mar 20 20:05:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d44_30569/03_2024/7d44_30569_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d44_30569/03_2024/7d44_30569.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d44_30569/03_2024/7d44_30569.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d44_30569/03_2024/7d44_30569.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d44_30569/03_2024/7d44_30569_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d44_30569/03_2024/7d44_30569_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 2 5.49 5 S 142 5.16 5 C 17918 2.51 5 N 4998 2.21 5 O 5331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 8": "OE1" <-> "OE2" Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A ARG 147": "NH1" <-> "NH2" Residue "A TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A TYR 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 74": "NH1" <-> "NH2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C PHE 177": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 202": "OE1" <-> "OE2" Residue "C PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 281": "OE1" <-> "OE2" Residue "C TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 338": "NH1" <-> "NH2" Residue "C TYR 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 347": "OD1" <-> "OD2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 63": "NH1" <-> "NH2" Residue "D PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 193": "OE1" <-> "OE2" Residue "D PHE 288": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 301": "OD1" <-> "OD2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 133": "NH1" <-> "NH2" Residue "E ARG 155": "NH1" <-> "NH2" Residue "E ASP 161": "OD1" <-> "OD2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E ASP 177": "OD1" <-> "OD2" Residue "E ARG 192": "NH1" <-> "NH2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E PHE 214": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 286": "NH1" <-> "NH2" Residue "F TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 49": "OE1" <-> "OE2" Residue "F TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 100": "OD1" <-> "OD2" Residue "F TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 133": "NH1" <-> "NH2" Residue "F PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 178": "OE1" <-> "OE2" Residue "F ARG 192": "NH1" <-> "NH2" Residue "F PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 288": "OD1" <-> "OD2" Residue "G ASP 172": "OD1" <-> "OD2" Residue "G TYR 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 305": "OD1" <-> "OD2" Residue "G TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 344": "NH1" <-> "NH2" Residue "G PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 417": "NH1" <-> "NH2" Residue "G PHE 443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 446": "NH1" <-> "NH2" Residue "G ASP 450": "OD1" <-> "OD2" Residue "G PHE 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 517": "NH1" <-> "NH2" Residue "H PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 305": "OD1" <-> "OD2" Residue "H TYR 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 344": "NH1" <-> "NH2" Residue "H TYR 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 417": "NH1" <-> "NH2" Residue "H ARG 446": "NH1" <-> "NH2" Residue "H ASP 458": "OD1" <-> "OD2" Residue "H ASP 459": "OD1" <-> "OD2" Residue "H ASP 490": "OD1" <-> "OD2" Residue "H ARG 517": "NH1" <-> "NH2" Residue "I ASP 53": "OD1" <-> "OD2" Residue "I ARG 65": "NH1" <-> "NH2" Residue "I TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 90": "OE1" <-> "OE2" Residue "I PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 154": "OD1" <-> "OD2" Residue "I ASP 199": "OD1" <-> "OD2" Residue "I ASP 206": "OD1" <-> "OD2" Residue "I PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 236": "OD1" <-> "OD2" Residue "I ASP 246": "OD1" <-> "OD2" Residue "I PHE 260": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 269": "NH1" <-> "NH2" Residue "I PHE 272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 299": "NH1" <-> "NH2" Residue "I ASP 461": "OD1" <-> "OD2" Residue "J ASP 50": "OD1" <-> "OD2" Residue "J ARG 65": "NH1" <-> "NH2" Residue "J TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 139": "OD1" <-> "OD2" Residue "J ASP 154": "OD1" <-> "OD2" Residue "J ARG 195": "NH1" <-> "NH2" Residue "J ARG 211": "NH1" <-> "NH2" Residue "J PHE 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 236": "OD1" <-> "OD2" Residue "J PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 269": "NH1" <-> "NH2" Residue "J ARG 299": "NH1" <-> "NH2" Residue "J TYR 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 312": "OD1" <-> "OD2" Residue "J ARG 316": "NH1" <-> "NH2" Residue "J TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 418": "OE1" <-> "OE2" Residue "J ASP 462": "OD1" <-> "OD2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 28391 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2262 Classifications: {'peptide': 293} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2247 Classifications: {'peptide': 291} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2476 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "D" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2538 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2430 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 10, 'TRANS': 332} Chain breaks: 4 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 99 Chain: "F" Number of atoms: 2429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2429 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 10, 'TRANS': 332} Chain breaks: 4 Unresolved non-hydrogen bonds: 249 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 188 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 6, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 100 Chain: "G" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "H" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "I" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3358 Classifications: {'peptide': 427} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 408} Chain: "J" Number of atoms: 3373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3373 Classifications: {'peptide': 429} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 409} Chain: "K" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 889 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 4, 'TRANS': 171} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 585 Unresolved non-hydrogen angles: 743 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 18, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 340 Chain: "L" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 889 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 4, 'TRANS': 171} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 585 Unresolved non-hydrogen angles: 743 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 18, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 340 Time building chain proxies: 14.01, per 1000 atoms: 0.49 Number of scatterers: 28391 At special positions: 0 Unit cell: (164.64, 169.05, 191.1, 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 142 16.00 P 2 15.00 O 5331 8.00 N 4998 7.00 C 17918 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: 10.64 Conformation dependent library (CDL) restraints added in 5.0 seconds 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7258 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 136 helices and 37 sheets defined 36.4% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.98 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 Processing helix chain 'A' and resid 22 through 35 Processing helix chain 'A' and resid 43 through 57 WARNING: missing atoms! Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 87 through 115 removed outlier: 4.472A pdb=" N ARG A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 160 through 171 removed outlier: 4.232A pdb=" N LEU A 171 " --> pdb=" O ALA A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 188 removed outlier: 3.674A pdb=" N VAL A 183 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLY A 184 " --> pdb=" O ALA A 181 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE A 186 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU A 188 " --> pdb=" O TYR A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 221 Processing helix chain 'A' and resid 243 through 245 No H-bonds generated for 'chain 'A' and resid 243 through 245' Processing helix chain 'A' and resid 248 through 251 No H-bonds generated for 'chain 'A' and resid 248 through 251' Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.931A pdb=" N SER A 297 " --> pdb=" O PRO A 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 16 removed outlier: 5.019A pdb=" N GLU B 8 " --> pdb=" O LYS B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 36 Processing helix chain 'B' and resid 43 through 46 No H-bonds generated for 'chain 'B' and resid 43 through 46' Processing helix chain 'B' and resid 48 through 59 removed outlier: 4.295A pdb=" N GLY B 58 " --> pdb=" O GLU B 54 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL B 59 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 77 removed outlier: 3.962A pdb=" N SER B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 115 removed outlier: 4.105A pdb=" N ARG B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASN B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 143 removed outlier: 4.002A pdb=" N ALA B 140 " --> pdb=" O ARG B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 171 removed outlier: 4.280A pdb=" N LEU B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 186 through 189 Processing helix chain 'B' and resid 210 through 222 removed outlier: 4.107A pdb=" N ASN B 213 " --> pdb=" O ILE B 210 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N GLN B 214 " --> pdb=" O GLY B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 251 No H-bonds generated for 'chain 'B' and resid 248 through 251' Processing helix chain 'B' and resid 293 through 304 Processing helix chain 'C' and resid 9 through 23 Processing helix chain 'C' and resid 31 through 47 Processing helix chain 'C' and resid 54 through 71 Processing helix chain 'C' and resid 77 through 95 Processing helix chain 'C' and resid 129 through 157 removed outlier: 3.594A pdb=" N GLY C 146 " --> pdb=" O VAL C 142 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N MET C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LEU C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLU C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 181 Processing helix chain 'C' and resid 198 through 210 removed outlier: 4.413A pdb=" N LEU C 207 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 228 removed outlier: 4.224A pdb=" N PHE C 223 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N SER C 227 " --> pdb=" O ALA C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 Processing helix chain 'C' and resid 271 through 273 No H-bonds generated for 'chain 'C' and resid 271 through 273' Processing helix chain 'C' and resid 297 through 299 No H-bonds generated for 'chain 'C' and resid 297 through 299' Processing helix chain 'C' and resid 301 through 304 Processing helix chain 'C' and resid 318 through 320 No H-bonds generated for 'chain 'C' and resid 318 through 320' Processing helix chain 'C' and resid 335 through 343 Processing helix chain 'C' and resid 346 through 350 removed outlier: 4.034A pdb=" N HIS C 349 " --> pdb=" O PRO C 346 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL C 350 " --> pdb=" O ASP C 347 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 346 through 350' Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 31 through 47 Processing helix chain 'D' and resid 54 through 71 Processing helix chain 'D' and resid 76 through 95 Processing helix chain 'D' and resid 128 through 145 Processing helix chain 'D' and resid 147 through 158 removed outlier: 4.720A pdb=" N GLN D 154 " --> pdb=" O ASN D 150 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLU D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N HIS D 158 " --> pdb=" O GLN D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 181 Processing helix chain 'D' and resid 200 through 210 removed outlier: 4.120A pdb=" N ALA D 210 " --> pdb=" O ASN D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 228 removed outlier: 5.157A pdb=" N SER D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N ARG D 228 " --> pdb=" O ALA D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 260 Processing helix chain 'D' and resid 271 through 273 No H-bonds generated for 'chain 'D' and resid 271 through 273' Processing helix chain 'D' and resid 279 through 281 No H-bonds generated for 'chain 'D' and resid 279 through 281' Processing helix chain 'D' and resid 291 through 293 No H-bonds generated for 'chain 'D' and resid 291 through 293' Processing helix chain 'D' and resid 301 through 304 Processing helix chain 'D' and resid 339 through 343 Processing helix chain 'D' and resid 346 through 348 No H-bonds generated for 'chain 'D' and resid 346 through 348' Processing helix chain 'E' and resid 35 through 45 Proline residue: E 39 - end of helix removed outlier: 4.330A pdb=" N LEU E 42 " --> pdb=" O TYR E 38 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU E 43 " --> pdb=" O PRO E 39 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 66 No H-bonds generated for 'chain 'E' and resid 63 through 66' Processing helix chain 'E' and resid 86 through 96 Proline residue: E 95 - end of helix Processing helix chain 'E' and resid 114 through 123 Processing helix chain 'E' and resid 210 through 216 Processing helix chain 'E' and resid 224 through 227 No H-bonds generated for 'chain 'E' and resid 224 through 227' Processing helix chain 'E' and resid 229 through 237 removed outlier: 4.549A pdb=" N PHE E 237 " --> pdb=" O VAL E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 294 removed outlier: 4.329A pdb=" N TRP E 290 " --> pdb=" O ARG E 286 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU E 293 " --> pdb=" O ARG E 289 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N SER E 294 " --> pdb=" O TRP E 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 45 Processing helix chain 'F' and resid 63 through 67 Processing helix chain 'F' and resid 86 through 93 Processing helix chain 'F' and resid 114 through 122 Processing helix chain 'F' and resid 184 through 189 Processing helix chain 'F' and resid 209 through 217 Processing helix chain 'F' and resid 224 through 235 removed outlier: 5.256A pdb=" N ILE F 229 " --> pdb=" O ARG F 225 " (cutoff:3.500A) Proline residue: F 230 - end of helix Processing helix chain 'F' and resid 279 through 291 removed outlier: 3.776A pdb=" N ASN F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 180 No H-bonds generated for 'chain 'G' and resid 178 through 180' Processing helix chain 'G' and resid 192 through 194 No H-bonds generated for 'chain 'G' and resid 192 through 194' Processing helix chain 'G' and resid 205 through 215 Processing helix chain 'G' and resid 222 through 237 Processing helix chain 'G' and resid 248 through 266 removed outlier: 4.991A pdb=" N VAL G 253 " --> pdb=" O SER G 249 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 271 through 286 Processing helix chain 'G' and resid 293 through 310 Processing helix chain 'G' and resid 313 through 325 removed outlier: 4.286A pdb=" N GLN G 325 " --> pdb=" O ARG G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 351 Processing helix chain 'G' and resid 369 through 379 removed outlier: 3.960A pdb=" N ALA G 379 " --> pdb=" O SER G 375 " (cutoff:3.500A) Processing helix chain 'G' and resid 388 through 393 removed outlier: 4.674A pdb=" N SER G 392 " --> pdb=" O PRO G 389 " (cutoff:3.500A) Processing helix chain 'G' and resid 418 through 430 removed outlier: 4.621A pdb=" N GLN G 422 " --> pdb=" O VAL G 418 " (cutoff:3.500A) Processing helix chain 'G' and resid 460 through 462 No H-bonds generated for 'chain 'G' and resid 460 through 462' Processing helix chain 'G' and resid 509 through 515 Proline residue: G 513 - end of helix Processing helix chain 'H' and resid 178 through 180 No H-bonds generated for 'chain 'H' and resid 178 through 180' Processing helix chain 'H' and resid 192 through 195 Processing helix chain 'H' and resid 205 through 215 Processing helix chain 'H' and resid 222 through 239 removed outlier: 3.745A pdb=" N ASP H 239 " --> pdb=" O GLN H 235 " (cutoff:3.500A) Processing helix chain 'H' and resid 248 through 266 removed outlier: 4.573A pdb=" N VAL H 253 " --> pdb=" O SER H 249 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 271 through 286 Processing helix chain 'H' and resid 293 through 310 Processing helix chain 'H' and resid 313 through 326 removed outlier: 4.754A pdb=" N GLN H 325 " --> pdb=" O ARG H 321 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS H 326 " --> pdb=" O PHE H 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 349 Processing helix chain 'H' and resid 370 through 379 removed outlier: 4.152A pdb=" N ALA H 379 " --> pdb=" O SER H 375 " (cutoff:3.500A) Processing helix chain 'H' and resid 388 through 396 removed outlier: 5.744A pdb=" N SER H 392 " --> pdb=" O PRO H 389 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N LEU H 395 " --> pdb=" O SER H 392 " (cutoff:3.500A) Proline residue: H 396 - end of helix Processing helix chain 'H' and resid 420 through 429 Processing helix chain 'H' and resid 460 through 462 No H-bonds generated for 'chain 'H' and resid 460 through 462' Processing helix chain 'H' and resid 509 through 511 No H-bonds generated for 'chain 'H' and resid 509 through 511' Processing helix chain 'H' and resid 513 through 516 No H-bonds generated for 'chain 'H' and resid 513 through 516' Processing helix chain 'I' and resid 59 through 62 No H-bonds generated for 'chain 'I' and resid 59 through 62' Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 99 through 107 Processing helix chain 'I' and resid 131 through 140 Processing helix chain 'I' and resid 162 through 175 Processing helix chain 'I' and resid 228 through 233 Processing helix chain 'I' and resid 254 through 261 Processing helix chain 'I' and resid 269 through 278 Processing helix chain 'I' and resid 303 through 313 Processing helix chain 'I' and resid 331 through 333 No H-bonds generated for 'chain 'I' and resid 331 through 333' Processing helix chain 'I' and resid 339 through 341 No H-bonds generated for 'chain 'I' and resid 339 through 341' Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'J' and resid 65 through 67 No H-bonds generated for 'chain 'J' and resid 65 through 67' Processing helix chain 'J' and resid 75 through 86 Processing helix chain 'J' and resid 99 through 108 removed outlier: 4.407A pdb=" N LYS J 108 " --> pdb=" O GLU J 104 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 141 Processing helix chain 'J' and resid 162 through 174 Processing helix chain 'J' and resid 197 through 199 No H-bonds generated for 'chain 'J' and resid 197 through 199' Processing helix chain 'J' and resid 228 through 233 Processing helix chain 'J' and resid 254 through 262 removed outlier: 4.260A pdb=" N ASP J 262 " --> pdb=" O GLN J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 269 through 278 Processing helix chain 'J' and resid 303 through 315 removed outlier: 3.966A pdb=" N ARG J 315 " --> pdb=" O ALA J 311 " (cutoff:3.500A) Processing helix chain 'J' and resid 331 through 333 No H-bonds generated for 'chain 'J' and resid 331 through 333' Processing helix chain 'J' and resid 339 through 341 No H-bonds generated for 'chain 'J' and resid 339 through 341' Processing helix chain 'K' and resid 54 through 56 No H-bonds generated for 'chain 'K' and resid 54 through 56' Processing helix chain 'K' and resid 60 through 64 Processing helix chain 'K' and resid 91 through 117 Processing helix chain 'K' and resid 123 through 140 Processing helix chain 'K' and resid 146 through 156 removed outlier: 4.989A pdb=" N VAL K 156 " --> pdb=" O PHE K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 169 through 178 Processing helix chain 'L' and resid 53 through 56 removed outlier: 3.738A pdb=" N ARG L 56 " --> pdb=" O ARG L 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 53 through 56' Processing helix chain 'L' and resid 91 through 117 removed outlier: 3.933A pdb=" N VAL L 117 " --> pdb=" O HIS L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 123 through 140 Processing helix chain 'L' and resid 148 through 154 Processing helix chain 'L' and resid 163 through 165 No H-bonds generated for 'chain 'L' and resid 163 through 165' Processing helix chain 'L' and resid 169 through 178 Processing sheet with id= A, first strand: chain 'A' and resid 123 through 126 Processing sheet with id= B, first strand: chain 'A' and resid 193 through 196 removed outlier: 6.653A pdb=" N LEU A 283 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 206 through 209 Processing sheet with id= D, first strand: chain 'B' and resid 123 through 127 removed outlier: 7.540A pdb=" N VAL B 152 " --> pdb=" O PRO B 174 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR B 176 " --> pdb=" O VAL B 152 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 193 through 196 removed outlier: 3.518A pdb=" N VAL B 229 " --> pdb=" O VAL B 195 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU B 283 " --> pdb=" O VAL B 228 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 207 through 209 Processing sheet with id= G, first strand: chain 'C' and resid 329 through 332 removed outlier: 3.782A pdb=" N LYS C 231 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ILE C 168 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N HIS C 188 " --> pdb=" O ILE C 165 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N THR C 167 " --> pdb=" O HIS C 188 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE C 190 " --> pdb=" O THR C 167 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 246 through 248 Processing sheet with id= I, first strand: chain 'D' and resid 189 through 193 Processing sheet with id= J, first strand: chain 'D' and resid 231 through 234 removed outlier: 7.310A pdb=" N ILE D 234 " --> pdb=" O PRO D 264 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE D 266 " --> pdb=" O ILE D 234 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'D' and resid 246 through 248 Processing sheet with id= L, first strand: chain 'D' and resid 324 through 326 Processing sheet with id= M, first strand: chain 'E' and resid 100 through 103 removed outlier: 7.307A pdb=" N VAL E 76 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 8.205A pdb=" N THR E 55 " --> pdb=" O VAL E 76 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N ILE E 78 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 129 through 132 removed outlier: 7.644A pdb=" N TYR E 264 " --> pdb=" O MET E 130 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N MET E 132 " --> pdb=" O TYR E 264 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N PHE E 266 " --> pdb=" O MET E 132 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'E' and resid 193 through 196 removed outlier: 5.760A pdb=" N ASP E 161 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU E 167 " --> pdb=" O ASP E 161 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 52 through 54 removed outlier: 6.324A pdb=" N VAL F 76 " --> pdb=" O VAL F 53 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'F' and resid 101 through 103 Processing sheet with id= R, first strand: chain 'F' and resid 169 through 171 Processing sheet with id= S, first strand: chain 'G' and resid 360 through 362 removed outlier: 3.517A pdb=" N LEU G 386 " --> pdb=" O VAL G 360 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ASP G 362 " --> pdb=" O LEU G 386 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'G' and resid 414 through 417 Processing sheet with id= U, first strand: chain 'G' and resid 500 through 502 Processing sheet with id= V, first strand: chain 'H' and resid 401 through 404 Processing sheet with id= W, first strand: chain 'H' and resid 414 through 416 Processing sheet with id= X, first strand: chain 'H' and resid 500 through 502 Processing sheet with id= Y, first strand: chain 'I' and resid 149 through 151 removed outlier: 6.153A pdb=" N GLU I 90 " --> pdb=" O ALA I 45 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU I 47 " --> pdb=" O GLU I 90 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N PHE I 92 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N VAL I 119 " --> pdb=" O THR I 91 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N VAL I 93 " --> pdb=" O VAL I 119 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ARG I 121 " --> pdb=" O VAL I 93 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'I' and resid 155 through 157 Processing sheet with id= AA, first strand: chain 'I' and resid 288 through 292 Processing sheet with id= AB, first strand: chain 'I' and resid 239 through 241 Processing sheet with id= AC, first strand: chain 'I' and resid 373 through 375 Processing sheet with id= AD, first strand: chain 'J' and resid 44 through 48 removed outlier: 6.309A pdb=" N GLU J 90 " --> pdb=" O ALA J 45 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU J 47 " --> pdb=" O GLU J 90 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N PHE J 92 " --> pdb=" O LEU J 47 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'J' and resid 185 through 187 Processing sheet with id= AF, first strand: chain 'J' and resid 239 through 241 removed outlier: 5.631A pdb=" N ASP J 206 " --> pdb=" O VAL J 212 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N VAL J 212 " --> pdb=" O ASP J 206 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'J' and resid 390 through 392 Processing sheet with id= AH, first strand: chain 'K' and resid 67 through 71 removed outlier: 6.944A pdb=" N TYR K 32 " --> pdb=" O ARG K 24 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ILE K 82 " --> pdb=" O MET K 44 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP K 83 " --> pdb=" O ARG K 74 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG K 74 " --> pdb=" O ASP K 83 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N SER K 85 " --> pdb=" O VAL K 72 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N VAL K 72 " --> pdb=" O SER K 85 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 19 through 23 removed outlier: 3.670A pdb=" N ARG L 66 " --> pdb=" O VAL L 23 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'L' and resid 30 through 34 Processing sheet with id= AK, first strand: chain 'L' and resid 74 through 76 978 hydrogen bonds defined for protein. 2736 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.35 Time building geometry restraints manager: 11.58 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: 9599 1.34 - 1.46: 5112 1.46 - 1.58: 13932 1.58 - 1.70: 8 1.70 - 1.81: 216 Bond restraints: 28867 Sorted by residual: bond pdb=" C SER J 188 " pdb=" N SER J 189 " ideal model delta sigma weight residual 1.329 1.252 0.077 1.86e-02 2.89e+03 1.71e+01 bond pdb=" CA LEU D 303 " pdb=" C LEU D 303 " ideal model delta sigma weight residual 1.523 1.481 0.042 1.34e-02 5.57e+03 9.89e+00 bond pdb=" CA GLU D 157 " pdb=" C GLU D 157 " ideal model delta sigma weight residual 1.524 1.483 0.040 1.29e-02 6.01e+03 9.65e+00 bond pdb=" CA SER H 481 " pdb=" C SER H 481 " ideal model delta sigma weight residual 1.523 1.488 0.035 1.34e-02 5.57e+03 6.98e+00 bond pdb=" CA HIS D 260 " pdb=" C HIS D 260 " ideal model delta sigma weight residual 1.522 1.489 0.033 1.40e-02 5.10e+03 5.71e+00 ... (remaining 28862 not shown) Histogram of bond angle deviations from ideal: 98.71 - 105.78: 574 105.78 - 112.85: 16034 112.85 - 119.92: 9384 119.92 - 126.99: 12965 126.99 - 134.06: 268 Bond angle restraints: 39225 Sorted by residual: angle pdb=" C PHE K 12 " pdb=" N PRO K 13 " pdb=" CA PRO K 13 " ideal model delta sigma weight residual 119.84 131.02 -11.18 1.25e+00 6.40e-01 8.00e+01 angle pdb=" N GLU K 14 " pdb=" CA GLU K 14 " pdb=" C GLU K 14 " ideal model delta sigma weight residual 108.74 116.72 -7.98 1.38e+00 5.25e-01 3.35e+01 angle pdb=" C GLU K 14 " pdb=" N VAL K 15 " pdb=" CA VAL K 15 " ideal model delta sigma weight residual 120.35 128.24 -7.89 1.39e+00 5.18e-01 3.22e+01 angle pdb=" C LEU C 178 " pdb=" N LYS C 179 " pdb=" CA LYS C 179 " ideal model delta sigma weight residual 121.94 111.23 10.71 2.00e+00 2.50e-01 2.87e+01 angle pdb=" N VAL C 225 " pdb=" CA VAL C 225 " pdb=" C VAL C 225 " ideal model delta sigma weight residual 113.20 108.63 4.57 9.60e-01 1.09e+00 2.26e+01 ... (remaining 39220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 15567 17.51 - 35.03: 1610 35.03 - 52.54: 288 52.54 - 70.06: 34 70.06 - 87.57: 22 Dihedral angle restraints: 17521 sinusoidal: 6374 harmonic: 11147 Sorted by residual: dihedral pdb=" CA GLU K 14 " pdb=" C GLU K 14 " pdb=" N VAL K 15 " pdb=" CA VAL K 15 " ideal model delta harmonic sigma weight residual -180.00 -137.21 -42.79 0 5.00e+00 4.00e-02 7.32e+01 dihedral pdb=" CA HIS D 125 " pdb=" C HIS D 125 " pdb=" N TYR D 126 " pdb=" CA TYR D 126 " ideal model delta harmonic sigma weight residual -180.00 -153.91 -26.09 0 5.00e+00 4.00e-02 2.72e+01 dihedral pdb=" CA SER C 284 " pdb=" C SER C 284 " pdb=" N PHE C 285 " pdb=" CA PHE C 285 " ideal model delta harmonic sigma weight residual 180.00 -154.08 -25.92 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 17518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 2669 0.036 - 0.073: 1333 0.073 - 0.109: 493 0.109 - 0.145: 151 0.145 - 0.182: 11 Chirality restraints: 4657 Sorted by residual: chirality pdb=" CA PRO A 293 " pdb=" N PRO A 293 " pdb=" C PRO A 293 " pdb=" CB PRO A 293 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA VAL I 238 " pdb=" N VAL I 238 " pdb=" C VAL I 238 " pdb=" CB VAL I 238 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.05e-01 chirality pdb=" CA ILE A 207 " pdb=" N ILE A 207 " pdb=" C ILE A 207 " pdb=" CB ILE A 207 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.87e-01 ... (remaining 4654 not shown) Planarity restraints: 5083 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 345 " 0.047 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO D 346 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO D 346 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 346 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 395 " 0.045 5.00e-02 4.00e+02 6.82e-02 7.44e+00 pdb=" N PRO H 396 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO H 396 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO H 396 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 395 " -0.043 5.00e-02 4.00e+02 6.53e-02 6.82e+00 pdb=" N PRO G 396 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO G 396 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 396 " -0.037 5.00e-02 4.00e+02 ... (remaining 5080 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 546 2.62 - 3.19: 28611 3.19 - 3.76: 43901 3.76 - 4.33: 59257 4.33 - 4.90: 95856 Nonbonded interactions: 228171 Sorted by model distance: nonbonded pdb=" OG SER G 416 " pdb=" OG1 THR G 420 " model vdw 2.049 2.440 nonbonded pdb=" OD2 ASP F 161 " pdb=" OG1 THR F 163 " model vdw 2.089 2.440 nonbonded pdb=" O ASP F 288 " pdb=" N ASP F 292 " model vdw 2.111 2.520 nonbonded pdb=" OG SER J 130 " pdb=" OE1 GLN J 267 " model vdw 2.113 2.440 nonbonded pdb=" ND2 ASN A 203 " pdb=" OH TYR A 275 " model vdw 2.123 2.520 ... (remaining 228166 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 1 through 27 or (resid 28 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name NE or name CZ )) or resid 29 \ through 253 or resid 268 through 305)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 8 through 343 or (resid 344 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 345 through 351)) selection = (chain 'D' and (resid 8 through 98 or resid 126 through 351)) } ncs_group { reference = (chain 'E' and (resid 1 through 263 or (resid 264 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 265 through 444)) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = (chain 'J' and resid 41 through 467) } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 7.130 Check model and map are aligned: 0.380 Set scattering table: 0.210 Process input model: 70.630 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 : 0.006 0.091 28867 Z= 0.397 Angle : 0.857 11.180 39225 Z= 0.504 Chirality : 0.049 0.182 4657 Planarity : 0.005 0.072 5083 Dihedral : 14.780 87.573 10263 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 16.34 % Favored : 83.61 % Rotamer: Outliers : 0.28 % Allowed : 9.91 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.25 (0.11), residues: 3771 helix: -2.48 (0.11), residues: 1365 sheet: -4.09 (0.20), residues: 409 loop : -4.24 (0.11), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 272 HIS 0.010 0.001 HIS B 128 PHE 0.021 0.002 PHE D 177 TYR 0.020 0.002 TYR E 231 ARG 0.009 0.001 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 366 time to evaluate : 3.356 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 7 ILE cc_start: 0.9101 (pt) cc_final: 0.8858 (mm) REVERT: A 187 MET cc_start: 0.7954 (tpp) cc_final: 0.7141 (tpp) REVERT: B 93 MET cc_start: 0.7170 (mmp) cc_final: 0.6474 (mmp) REVERT: C 34 MET cc_start: 0.7750 (mtm) cc_final: 0.7328 (mtm) REVERT: C 148 MET cc_start: 0.7762 (ttm) cc_final: 0.7426 (ttm) REVERT: C 217 MET cc_start: 0.6672 (ptt) cc_final: 0.6414 (ptt) REVERT: C 340 MET cc_start: 0.8157 (tmm) cc_final: 0.7881 (tmm) REVERT: D 226 MET cc_start: 0.8453 (tpt) cc_final: 0.7885 (tpp) REVERT: D 259 LYS cc_start: 0.8611 (ttpp) cc_final: 0.8073 (tptt) REVERT: E 69 MET cc_start: 0.6604 (tmm) cc_final: 0.6186 (tmm) REVERT: E 274 ASN cc_start: 0.7604 (m-40) cc_final: 0.7301 (m110) REVERT: F 84 MET cc_start: 0.5746 (mtt) cc_final: 0.5188 (mtt) REVERT: F 210 TYR cc_start: 0.7562 (p90) cc_final: 0.5285 (t80) REVERT: F 267 ILE cc_start: 0.7302 (pt) cc_final: 0.7088 (pt) REVERT: G 212 LEU cc_start: 0.8562 (tp) cc_final: 0.8318 (tt) REVERT: G 214 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.8171 (m-10) REVERT: G 216 GLN cc_start: 0.8084 (mm110) cc_final: 0.7617 (mp10) REVERT: G 467 ARG cc_start: 0.5816 (tpm170) cc_final: 0.4822 (tpp-160) REVERT: H 172 ASP cc_start: 0.7068 (t0) cc_final: 0.6809 (t0) outliers start: 8 outliers final: 5 residues processed: 373 average time/residue: 0.3997 time to fit residues: 235.2595 Evaluate side-chains 254 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 248 time to evaluate : 3.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain G residue 214 TYR Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain J residue 400 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 318 optimal weight: 0.0370 chunk 285 optimal weight: 0.9980 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 0.2980 chunk 192 optimal weight: 0.9990 chunk 152 optimal weight: 20.0000 chunk 295 optimal weight: 5.9990 chunk 114 optimal weight: 0.9980 chunk 179 optimal weight: 20.0000 chunk 219 optimal weight: 2.9990 chunk 342 optimal weight: 2.9990 overall best weight: 0.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 156 GLN B 208 ASN B 213 ASN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS D 119 ASN D 125 HIS D 158 HIS ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 HIS E 274 ASN F 60 GLN ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN F 283 ASN G 166 GLN G 189 GLN G 213 GLN G 216 GLN G 254 ASN G 265 GLN G 281 ASN G 325 GLN G 430 HIS ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 479 HIS H 194 GLN H 265 GLN H 274 HIS H 347 GLN H 430 HIS ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 214 HIS ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 255 GLN ** I 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 388 ASN J 44 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 158 ASN J 279 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 28867 Z= 0.206 Angle : 0.638 9.464 39225 Z= 0.329 Chirality : 0.045 0.181 4657 Planarity : 0.005 0.069 5083 Dihedral : 5.907 49.382 4099 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.41 % Favored : 90.56 % Rotamer: Outliers : 2.28 % Allowed : 16.60 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.12), residues: 3771 helix: -1.04 (0.13), residues: 1361 sheet: -3.77 (0.20), residues: 417 loop : -3.54 (0.12), residues: 1993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 282 HIS 0.005 0.001 HIS J 337 PHE 0.022 0.002 PHE E 48 TYR 0.012 0.001 TYR J 128 ARG 0.008 0.000 ARG I 171 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 304 time to evaluate : 3.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.8266 (ttm) cc_final: 0.8057 (ttp) REVERT: B 93 MET cc_start: 0.7380 (mmp) cc_final: 0.6554 (mmp) REVERT: B 244 GLN cc_start: 0.7875 (tp40) cc_final: 0.7643 (tp40) REVERT: C 34 MET cc_start: 0.7698 (mtm) cc_final: 0.7268 (mtm) REVERT: C 148 MET cc_start: 0.7825 (ttm) cc_final: 0.7591 (ttm) REVERT: C 217 MET cc_start: 0.6526 (ptt) cc_final: 0.6211 (ptt) REVERT: C 340 MET cc_start: 0.8064 (tmm) cc_final: 0.7754 (tmm) REVERT: D 226 MET cc_start: 0.8584 (tpt) cc_final: 0.7906 (tpp) REVERT: D 259 LYS cc_start: 0.8311 (ttpp) cc_final: 0.7803 (tptt) REVERT: E 69 MET cc_start: 0.6548 (tmm) cc_final: 0.5925 (tmm) REVERT: F 210 TYR cc_start: 0.7396 (p90) cc_final: 0.4964 (t80) REVERT: G 212 LEU cc_start: 0.8405 (tp) cc_final: 0.8092 (tt) REVERT: G 214 TYR cc_start: 0.8411 (OUTLIER) cc_final: 0.7904 (m-10) REVERT: G 216 GLN cc_start: 0.8130 (mm-40) cc_final: 0.7703 (mp10) REVERT: G 386 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7682 (pp) REVERT: G 467 ARG cc_start: 0.5714 (tpm170) cc_final: 0.4775 (tpp-160) REVERT: H 499 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8251 (mm) REVERT: J 173 LYS cc_start: 0.6596 (ptmm) cc_final: 0.6124 (tptp) REVERT: J 224 PHE cc_start: 0.8055 (m-80) cc_final: 0.7390 (m-80) outliers start: 65 outliers final: 32 residues processed: 344 average time/residue: 0.3481 time to fit residues: 200.7354 Evaluate side-chains 287 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 252 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 203 HIS Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 216 MET Chi-restraints excluded: chain G residue 166 GLN Chi-restraints excluded: chain G residue 214 TYR Chi-restraints excluded: chain G residue 386 LEU Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain G residue 435 LEU Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 400 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 190 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 284 optimal weight: 3.9990 chunk 233 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 342 optimal weight: 0.0270 chunk 370 optimal weight: 5.9990 chunk 305 optimal weight: 0.7980 chunk 340 optimal weight: 0.3980 chunk 116 optimal weight: 1.9990 chunk 275 optimal weight: 0.0570 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** B 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN D 125 HIS ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 236 GLN F 236 GLN F 274 ASN ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 285 ASN ** I 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 28867 Z= 0.168 Angle : 0.589 7.864 39225 Z= 0.303 Chirality : 0.044 0.159 4657 Planarity : 0.004 0.062 5083 Dihedral : 5.413 48.807 4097 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.04 % Favored : 91.94 % Rotamer: Outliers : 2.49 % Allowed : 19.61 % Favored : 77.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.13), residues: 3771 helix: -0.27 (0.14), residues: 1366 sheet: -3.44 (0.21), residues: 418 loop : -3.06 (0.13), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 37 HIS 0.006 0.001 HIS A 116 PHE 0.019 0.001 PHE C 177 TYR 0.013 0.001 TYR A 185 ARG 0.005 0.000 ARG I 171 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 316 time to evaluate : 3.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8117 (tpp) cc_final: 0.7177 (tpp) REVERT: A 208 ASN cc_start: 0.7590 (t0) cc_final: 0.7348 (t0) REVERT: A 287 ASP cc_start: 0.7059 (OUTLIER) cc_final: 0.6000 (t0) REVERT: B 93 MET cc_start: 0.7536 (mmp) cc_final: 0.6586 (mmp) REVERT: B 104 ILE cc_start: 0.8039 (mm) cc_final: 0.7783 (mm) REVERT: B 187 MET cc_start: 0.8587 (tpt) cc_final: 0.8232 (mmm) REVERT: B 244 GLN cc_start: 0.7703 (tp40) cc_final: 0.7459 (tp40) REVERT: C 34 MET cc_start: 0.7567 (mtm) cc_final: 0.7205 (mtm) REVERT: C 148 MET cc_start: 0.7746 (ttm) cc_final: 0.7323 (tmm) REVERT: C 340 MET cc_start: 0.7892 (tmm) cc_final: 0.7635 (tmm) REVERT: D 125 HIS cc_start: 0.5194 (p90) cc_final: 0.4965 (p90) REVERT: D 166 MET cc_start: 0.7985 (mtp) cc_final: 0.7741 (mtp) REVERT: D 305 LYS cc_start: 0.8463 (mttp) cc_final: 0.7969 (mttp) REVERT: E 37 TRP cc_start: 0.7518 (t60) cc_final: 0.7131 (t-100) REVERT: E 69 MET cc_start: 0.6765 (tmm) cc_final: 0.6157 (tmm) REVERT: E 290 TRP cc_start: 0.7116 (t60) cc_final: 0.6682 (p90) REVERT: F 210 TYR cc_start: 0.7328 (p90) cc_final: 0.4937 (t80) REVERT: F 216 MET cc_start: 0.7820 (ttp) cc_final: 0.7555 (ttm) REVERT: G 195 PHE cc_start: 0.6083 (m-80) cc_final: 0.5729 (m-80) REVERT: G 214 TYR cc_start: 0.8224 (OUTLIER) cc_final: 0.7770 (m-10) REVERT: G 467 ARG cc_start: 0.5852 (tpm170) cc_final: 0.4741 (tpp-160) REVERT: H 207 MET cc_start: 0.7815 (mmp) cc_final: 0.7448 (mmp) REVERT: H 233 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.8147 (mt) REVERT: H 463 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8143 (mt) REVERT: H 499 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8264 (mm) REVERT: J 97 TRP cc_start: 0.7846 (t60) cc_final: 0.7595 (t60) REVERT: J 173 LYS cc_start: 0.6501 (ptmm) cc_final: 0.6103 (tptp) REVERT: J 183 MET cc_start: 0.8344 (mtp) cc_final: 0.7977 (ttt) REVERT: J 224 PHE cc_start: 0.8077 (m-80) cc_final: 0.7443 (m-80) REVERT: J 289 MET cc_start: 0.7462 (tmm) cc_final: 0.6755 (tmm) outliers start: 71 outliers final: 36 residues processed: 366 average time/residue: 0.3530 time to fit residues: 216.2010 Evaluate side-chains 305 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 264 time to evaluate : 3.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 319 GLU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 214 TYR Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 406 HIS Chi-restraints excluded: chain H residue 463 LEU Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 411 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 342 ILE Chi-restraints excluded: chain J residue 400 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 338 optimal weight: 0.0070 chunk 257 optimal weight: 1.9990 chunk 177 optimal weight: 0.0770 chunk 37 optimal weight: 3.9990 chunk 163 optimal weight: 7.9990 chunk 230 optimal weight: 0.8980 chunk 344 optimal weight: 30.0000 chunk 364 optimal weight: 0.5980 chunk 179 optimal weight: 20.0000 chunk 326 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN B 13 GLN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 138 ASN ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS C 277 GLN ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 ASN ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 304 HIS J 341 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.2281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28867 Z= 0.170 Angle : 0.573 8.263 39225 Z= 0.291 Chirality : 0.044 0.149 4657 Planarity : 0.004 0.062 5083 Dihedral : 5.219 57.635 4097 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.24 % Favored : 92.76 % Rotamer: Outliers : 3.15 % Allowed : 21.57 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.13), residues: 3771 helix: 0.15 (0.14), residues: 1367 sheet: -3.20 (0.22), residues: 420 loop : -2.84 (0.13), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 282 HIS 0.007 0.001 HIS I 192 PHE 0.034 0.002 PHE A 72 TYR 0.014 0.001 TYR A 185 ARG 0.004 0.000 ARG K 63 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 304 time to evaluate : 3.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 MET cc_start: 0.8005 (tpp) cc_final: 0.7404 (tpp) REVERT: A 208 ASN cc_start: 0.7423 (t0) cc_final: 0.7051 (t0) REVERT: A 215 MET cc_start: 0.8255 (ttm) cc_final: 0.8010 (ttp) REVERT: A 287 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.5941 (t0) REVERT: B 14 MET cc_start: 0.6721 (tpp) cc_final: 0.5917 (ttt) REVERT: B 244 GLN cc_start: 0.7676 (tp40) cc_final: 0.7412 (tp40) REVERT: C 34 MET cc_start: 0.7510 (mtm) cc_final: 0.7250 (mtm) REVERT: C 44 GLN cc_start: 0.7359 (tt0) cc_final: 0.7051 (tt0) REVERT: C 148 MET cc_start: 0.7728 (ttm) cc_final: 0.7317 (tmm) REVERT: C 340 MET cc_start: 0.7890 (tmm) cc_final: 0.7598 (tmm) REVERT: D 139 GLU cc_start: 0.7563 (tm-30) cc_final: 0.7300 (tm-30) REVERT: D 304 GLU cc_start: 0.7280 (pm20) cc_final: 0.6980 (pm20) REVERT: E 69 MET cc_start: 0.6571 (tmm) cc_final: 0.6044 (tmm) REVERT: E 132 MET cc_start: 0.7578 (mmm) cc_final: 0.7160 (mmm) REVERT: E 170 MET cc_start: 0.3824 (ppp) cc_final: 0.3508 (ppp) REVERT: E 290 TRP cc_start: 0.7070 (t60) cc_final: 0.6663 (p90) REVERT: F 210 TYR cc_start: 0.7322 (p90) cc_final: 0.4766 (t80) REVERT: G 214 TYR cc_start: 0.8139 (OUTLIER) cc_final: 0.7727 (m-10) REVERT: G 255 LYS cc_start: 0.8428 (mmtp) cc_final: 0.8117 (tptt) REVERT: G 467 ARG cc_start: 0.5743 (tpm170) cc_final: 0.5059 (mmp80) REVERT: H 207 MET cc_start: 0.7808 (mmp) cc_final: 0.7388 (mmp) REVERT: H 233 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8144 (mt) REVERT: I 289 MET cc_start: 0.7433 (tmm) cc_final: 0.7163 (tmm) REVERT: J 173 LYS cc_start: 0.6636 (ptmm) cc_final: 0.6183 (tptp) REVERT: J 183 MET cc_start: 0.8380 (mtp) cc_final: 0.8025 (ttt) REVERT: J 224 PHE cc_start: 0.8073 (m-80) cc_final: 0.7343 (m-80) REVERT: J 289 MET cc_start: 0.7468 (tmm) cc_final: 0.6804 (tmm) REVERT: J 431 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.7985 (pp) REVERT: K 63 ARG cc_start: 0.6031 (mmp-170) cc_final: 0.5732 (mmp-170) outliers start: 90 outliers final: 46 residues processed: 366 average time/residue: 0.3432 time to fit residues: 208.9889 Evaluate side-chains 318 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 268 time to evaluate : 3.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 201 HIS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 214 TYR Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain G residue 398 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 406 HIS Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 226 PHE Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 411 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 421 GLU Chi-restraints excluded: chain J residue 431 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 303 optimal weight: 7.9990 chunk 206 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 271 optimal weight: 4.9990 chunk 150 optimal weight: 50.0000 chunk 310 optimal weight: 0.5980 chunk 251 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 186 optimal weight: 10.0000 chunk 327 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 GLN ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28867 Z= 0.194 Angle : 0.580 8.640 39225 Z= 0.295 Chirality : 0.044 0.154 4657 Planarity : 0.004 0.061 5083 Dihedral : 5.145 59.329 4097 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.93 % Favored : 92.07 % Rotamer: Outliers : 3.08 % Allowed : 23.14 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.13), residues: 3771 helix: 0.35 (0.14), residues: 1367 sheet: -3.07 (0.22), residues: 438 loop : -2.70 (0.13), residues: 1966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 282 HIS 0.005 0.001 HIS A 128 PHE 0.022 0.001 PHE C 177 TYR 0.012 0.001 TYR A 130 ARG 0.004 0.000 ARG A 132 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 285 time to evaluate : 3.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7452 (tt) REVERT: A 164 MET cc_start: 0.8586 (tpt) cc_final: 0.8245 (tpt) REVERT: A 187 MET cc_start: 0.8009 (tpp) cc_final: 0.7283 (tpp) REVERT: A 208 ASN cc_start: 0.7333 (t0) cc_final: 0.6969 (t0) REVERT: A 287 ASP cc_start: 0.7135 (OUTLIER) cc_final: 0.5945 (t0) REVERT: B 14 MET cc_start: 0.6960 (tpp) cc_final: 0.6559 (ttt) REVERT: B 93 MET cc_start: 0.7081 (mmp) cc_final: 0.6640 (mmp) REVERT: B 244 GLN cc_start: 0.7444 (tp40) cc_final: 0.7198 (tp40) REVERT: C 34 MET cc_start: 0.7764 (mtm) cc_final: 0.7338 (mtm) REVERT: C 68 MET cc_start: 0.7899 (mtp) cc_final: 0.7621 (mtm) REVERT: C 148 MET cc_start: 0.7720 (ttm) cc_final: 0.7301 (tmm) REVERT: C 340 MET cc_start: 0.7962 (tmm) cc_final: 0.7693 (tmm) REVERT: D 340 MET cc_start: 0.7513 (mmt) cc_final: 0.6803 (mmp) REVERT: E 44 GLU cc_start: 0.6211 (mm-30) cc_final: 0.6010 (mm-30) REVERT: E 69 MET cc_start: 0.6559 (tmm) cc_final: 0.5933 (tmm) REVERT: E 124 TYR cc_start: 0.7360 (m-10) cc_final: 0.7070 (m-10) REVERT: E 131 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8123 (tt) REVERT: E 170 MET cc_start: 0.4233 (ppp) cc_final: 0.3672 (ppp) REVERT: E 273 LEU cc_start: 0.3467 (OUTLIER) cc_final: 0.2805 (tp) REVERT: E 290 TRP cc_start: 0.7086 (t60) cc_final: 0.6665 (p90) REVERT: F 36 ILE cc_start: 0.6886 (mp) cc_final: 0.6339 (mm) REVERT: F 210 TYR cc_start: 0.7233 (p90) cc_final: 0.4696 (t80) REVERT: G 207 MET cc_start: 0.6801 (ttt) cc_final: 0.6471 (ttt) REVERT: G 214 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.7651 (m-10) REVERT: G 255 LYS cc_start: 0.8423 (mmtp) cc_final: 0.8122 (tptt) REVERT: G 467 ARG cc_start: 0.6179 (tpm170) cc_final: 0.5466 (mmp80) REVERT: H 233 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8129 (mt) REVERT: H 499 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8209 (mm) REVERT: I 205 VAL cc_start: 0.9249 (OUTLIER) cc_final: 0.8985 (m) REVERT: J 97 TRP cc_start: 0.7824 (t60) cc_final: 0.7147 (t60) REVERT: J 173 LYS cc_start: 0.6590 (ptmm) cc_final: 0.6120 (tptp) REVERT: J 183 MET cc_start: 0.8240 (mtp) cc_final: 0.7885 (ttt) REVERT: J 224 PHE cc_start: 0.8095 (m-80) cc_final: 0.7564 (m-80) REVERT: J 289 MET cc_start: 0.7530 (tmm) cc_final: 0.7053 (tmm) REVERT: J 431 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8047 (pp) outliers start: 88 outliers final: 59 residues processed: 344 average time/residue: 0.3468 time to fit residues: 200.3498 Evaluate side-chains 328 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 260 time to evaluate : 3.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 214 TYR Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 406 HIS Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 226 PHE Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 411 SER Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain J residue 200 ASN Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 421 GLU Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 431 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 122 optimal weight: 5.9990 chunk 328 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 364 optimal weight: 1.9990 chunk 302 optimal weight: 0.2980 chunk 168 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 120 optimal weight: 0.3980 chunk 191 optimal weight: 7.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN B 13 GLN ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 285 ASN I 410 GLN ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28867 Z= 0.190 Angle : 0.575 8.064 39225 Z= 0.291 Chirality : 0.044 0.151 4657 Planarity : 0.004 0.064 5083 Dihedral : 5.030 57.870 4095 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.89 % Allowed : 23.42 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.14), residues: 3771 helix: 0.53 (0.14), residues: 1355 sheet: -2.92 (0.22), residues: 445 loop : -2.57 (0.14), residues: 1971 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 282 HIS 0.004 0.001 HIS A 170 PHE 0.021 0.001 PHE C 177 TYR 0.020 0.001 TYR A 185 ARG 0.003 0.000 ARG K 63 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 275 time to evaluate : 3.587 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7460 (tt) REVERT: A 164 MET cc_start: 0.8557 (tpt) cc_final: 0.8215 (tpt) REVERT: A 187 MET cc_start: 0.8133 (tpp) cc_final: 0.7508 (tpp) REVERT: A 208 ASN cc_start: 0.7300 (t0) cc_final: 0.6983 (t0) REVERT: A 287 ASP cc_start: 0.7138 (OUTLIER) cc_final: 0.5955 (t0) REVERT: B 14 MET cc_start: 0.7337 (tpp) cc_final: 0.6922 (ttt) REVERT: B 244 GLN cc_start: 0.7597 (tp40) cc_final: 0.7335 (tp40) REVERT: C 34 MET cc_start: 0.7646 (mtm) cc_final: 0.7264 (mtm) REVERT: C 68 MET cc_start: 0.7914 (mtp) cc_final: 0.7633 (mtm) REVERT: C 148 MET cc_start: 0.7686 (ttm) cc_final: 0.7289 (tmm) REVERT: C 340 MET cc_start: 0.8009 (tmm) cc_final: 0.7743 (tmm) REVERT: D 301 ASP cc_start: 0.8228 (t0) cc_final: 0.7770 (t0) REVERT: D 340 MET cc_start: 0.7504 (mmt) cc_final: 0.6813 (mmp) REVERT: E 69 MET cc_start: 0.6567 (tmm) cc_final: 0.6364 (tmm) REVERT: E 124 TYR cc_start: 0.7466 (m-10) cc_final: 0.7244 (m-10) REVERT: E 131 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8153 (tt) REVERT: E 170 MET cc_start: 0.4232 (ppp) cc_final: 0.3647 (ppp) REVERT: E 268 LYS cc_start: 0.6786 (tppt) cc_final: 0.6477 (pttm) REVERT: E 290 TRP cc_start: 0.7118 (t60) cc_final: 0.6787 (p90) REVERT: F 36 ILE cc_start: 0.6856 (mp) cc_final: 0.6320 (mm) REVERT: F 199 LEU cc_start: 0.4377 (mt) cc_final: 0.4067 (mt) REVERT: F 210 TYR cc_start: 0.7200 (p90) cc_final: 0.4669 (t80) REVERT: G 214 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7694 (m-10) REVERT: G 255 LYS cc_start: 0.8337 (mmtp) cc_final: 0.8040 (tptt) REVERT: G 467 ARG cc_start: 0.6292 (tpm170) cc_final: 0.5153 (tpp-160) REVERT: H 233 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8213 (mt) REVERT: H 499 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8293 (mm) REVERT: I 205 VAL cc_start: 0.9163 (OUTLIER) cc_final: 0.8901 (m) REVERT: J 147 ASP cc_start: 0.8512 (m-30) cc_final: 0.8273 (m-30) REVERT: J 161 ILE cc_start: 0.9577 (OUTLIER) cc_final: 0.9372 (tt) REVERT: J 173 LYS cc_start: 0.6771 (ptmm) cc_final: 0.6205 (tptp) REVERT: J 183 MET cc_start: 0.8277 (mtp) cc_final: 0.7826 (ttt) REVERT: J 224 PHE cc_start: 0.8088 (m-80) cc_final: 0.7582 (m-80) REVERT: J 289 MET cc_start: 0.7462 (tmm) cc_final: 0.7008 (tmm) REVERT: J 431 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8039 (pp) outliers start: 111 outliers final: 74 residues processed: 355 average time/residue: 0.3351 time to fit residues: 201.9227 Evaluate side-chains 340 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 257 time to evaluate : 3.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 116 HIS Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 214 TYR Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 406 HIS Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 226 PHE Chi-restraints excluded: chain I residue 270 ASP Chi-restraints excluded: chain I residue 285 ASN Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 411 SER Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 200 ASN Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 421 GLU Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 431 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 351 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 207 optimal weight: 0.8980 chunk 266 optimal weight: 6.9990 chunk 206 optimal weight: 2.9990 chunk 307 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 363 optimal weight: 10.0000 chunk 227 optimal weight: 7.9990 chunk 221 optimal weight: 0.6980 chunk 167 optimal weight: 8.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN B 13 GLN ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 285 ASN I 384 HIS ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 28867 Z= 0.236 Angle : 0.599 14.241 39225 Z= 0.304 Chirality : 0.045 0.188 4657 Planarity : 0.004 0.064 5083 Dihedral : 5.110 57.376 4095 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 3.57 % Allowed : 24.51 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.14), residues: 3771 helix: 0.52 (0.14), residues: 1358 sheet: -2.89 (0.22), residues: 439 loop : -2.56 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 37 HIS 0.005 0.001 HIS B 128 PHE 0.024 0.001 PHE E 48 TYR 0.036 0.001 TYR F 94 ARG 0.003 0.000 ARG I 172 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 262 time to evaluate : 3.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7484 (tt) REVERT: A 164 MET cc_start: 0.8556 (tpt) cc_final: 0.8225 (tpt) REVERT: A 185 TYR cc_start: 0.8165 (t80) cc_final: 0.7963 (t80) REVERT: A 187 MET cc_start: 0.8080 (tpp) cc_final: 0.7406 (tpp) REVERT: A 208 ASN cc_start: 0.7439 (t0) cc_final: 0.7087 (t0) REVERT: A 287 ASP cc_start: 0.7232 (OUTLIER) cc_final: 0.6022 (t0) REVERT: B 14 MET cc_start: 0.7317 (tpp) cc_final: 0.6980 (ttt) REVERT: B 244 GLN cc_start: 0.7558 (tp40) cc_final: 0.7271 (tp40) REVERT: C 34 MET cc_start: 0.7715 (mtm) cc_final: 0.7302 (mtm) REVERT: C 68 MET cc_start: 0.7926 (mtp) cc_final: 0.7646 (mtm) REVERT: C 148 MET cc_start: 0.7725 (ttm) cc_final: 0.7325 (tmm) REVERT: C 340 MET cc_start: 0.8059 (tmm) cc_final: 0.7786 (tmm) REVERT: D 340 MET cc_start: 0.7620 (mmt) cc_final: 0.6914 (mmp) REVERT: E 37 TRP cc_start: 0.7593 (t60) cc_final: 0.7248 (t-100) REVERT: E 44 GLU cc_start: 0.6109 (mm-30) cc_final: 0.5796 (mm-30) REVERT: E 124 TYR cc_start: 0.7513 (m-10) cc_final: 0.7302 (m-10) REVERT: E 131 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8317 (tt) REVERT: E 170 MET cc_start: 0.4305 (ppp) cc_final: 0.3696 (ppp) REVERT: E 290 TRP cc_start: 0.7111 (t60) cc_final: 0.6762 (p90) REVERT: F 36 ILE cc_start: 0.6845 (mp) cc_final: 0.6302 (mm) REVERT: F 199 LEU cc_start: 0.4695 (mt) cc_final: 0.4345 (mt) REVERT: F 210 TYR cc_start: 0.7237 (p90) cc_final: 0.4671 (t80) REVERT: G 467 ARG cc_start: 0.6350 (tpm170) cc_final: 0.5197 (tpp-160) REVERT: H 172 ASP cc_start: 0.7221 (t0) cc_final: 0.6872 (t0) REVERT: H 233 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8147 (mt) REVERT: H 499 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8346 (mm) REVERT: I 205 VAL cc_start: 0.9081 (OUTLIER) cc_final: 0.8868 (m) REVERT: J 161 ILE cc_start: 0.9581 (OUTLIER) cc_final: 0.9364 (tt) REVERT: J 173 LYS cc_start: 0.6873 (ptmm) cc_final: 0.6360 (tptp) REVERT: J 183 MET cc_start: 0.8256 (mtp) cc_final: 0.7807 (ttt) REVERT: J 289 MET cc_start: 0.7668 (tmm) cc_final: 0.7271 (tmm) REVERT: J 431 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8110 (pp) outliers start: 102 outliers final: 75 residues processed: 333 average time/residue: 0.3496 time to fit residues: 198.1649 Evaluate side-chains 340 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 257 time to evaluate : 3.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 406 HIS Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 205 VAL Chi-restraints excluded: chain I residue 226 PHE Chi-restraints excluded: chain I residue 270 ASP Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 355 ILE Chi-restraints excluded: chain I residue 367 VAL Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 394 THR Chi-restraints excluded: chain I residue 411 SER Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 200 ASN Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 430 VAL Chi-restraints excluded: chain J residue 431 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 224 optimal weight: 4.9990 chunk 145 optimal weight: 0.0570 chunk 217 optimal weight: 0.9980 chunk 109 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 231 optimal weight: 0.8980 chunk 247 optimal weight: 0.5980 chunk 179 optimal weight: 10.0000 chunk 33 optimal weight: 0.0070 chunk 285 optimal weight: 0.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 223 ASN B 13 GLN ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 349 HIS ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 197 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28867 Z= 0.168 Angle : 0.574 12.771 39225 Z= 0.289 Chirality : 0.044 0.176 4657 Planarity : 0.004 0.064 5083 Dihedral : 4.881 55.187 4093 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 3.26 % Allowed : 25.18 % Favored : 71.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % 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: -1.94 (0.14), residues: 3771 helix: 0.63 (0.14), residues: 1366 sheet: -2.77 (0.23), residues: 438 loop : -2.42 (0.14), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 37 HIS 0.004 0.001 HIS A 170 PHE 0.032 0.001 PHE E 266 TYR 0.014 0.001 TYR A 185 ARG 0.003 0.000 ARG G 250 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 283 time to evaluate : 3.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7451 (tt) REVERT: A 164 MET cc_start: 0.8494 (tpt) cc_final: 0.8196 (tpt) REVERT: A 187 MET cc_start: 0.8059 (tpp) cc_final: 0.7768 (tpt) REVERT: A 208 ASN cc_start: 0.7085 (t0) cc_final: 0.6674 (t0) REVERT: A 287 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6028 (t0) REVERT: B 14 MET cc_start: 0.7313 (tpp) cc_final: 0.6933 (ttt) REVERT: B 187 MET cc_start: 0.8377 (tpt) cc_final: 0.7996 (mmm) REVERT: B 244 GLN cc_start: 0.7462 (tp40) cc_final: 0.7197 (tp40) REVERT: C 34 MET cc_start: 0.7655 (mtm) cc_final: 0.7282 (mtm) REVERT: C 68 MET cc_start: 0.7905 (mtp) cc_final: 0.7635 (mtm) REVERT: C 148 MET cc_start: 0.7593 (ttm) cc_final: 0.7203 (tmm) REVERT: C 299 GLU cc_start: 0.7773 (tp30) cc_final: 0.7530 (tp30) REVERT: C 340 MET cc_start: 0.7998 (tmm) cc_final: 0.7722 (tmm) REVERT: E 37 TRP cc_start: 0.7411 (t60) cc_final: 0.6896 (t-100) REVERT: E 44 GLU cc_start: 0.5924 (mm-30) cc_final: 0.5555 (mm-30) REVERT: E 69 MET cc_start: 0.6323 (tmm) cc_final: 0.5733 (tmm) REVERT: E 131 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8316 (tt) REVERT: E 170 MET cc_start: 0.4084 (ppp) cc_final: 0.3408 (ppp) REVERT: E 268 LYS cc_start: 0.6745 (tppt) cc_final: 0.6426 (pttm) REVERT: E 290 TRP cc_start: 0.7095 (t60) cc_final: 0.6748 (p90) REVERT: F 36 ILE cc_start: 0.6884 (mp) cc_final: 0.6334 (mm) REVERT: F 119 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.7800 (t70) REVERT: F 210 TYR cc_start: 0.7205 (p90) cc_final: 0.4689 (t80) REVERT: F 291 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: G 467 ARG cc_start: 0.6282 (tpm170) cc_final: 0.5262 (tpp-160) REVERT: H 233 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8242 (mt) REVERT: H 273 MET cc_start: 0.8467 (ptp) cc_final: 0.8251 (ptp) REVERT: H 499 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8270 (mm) REVERT: J 147 ASP cc_start: 0.8495 (m-30) cc_final: 0.8225 (m-30) REVERT: J 161 ILE cc_start: 0.9579 (OUTLIER) cc_final: 0.9371 (tt) REVERT: J 173 LYS cc_start: 0.7033 (ptmm) cc_final: 0.6480 (tptp) REVERT: J 224 PHE cc_start: 0.8086 (m-80) cc_final: 0.7283 (m-80) REVERT: J 289 MET cc_start: 0.7529 (tmm) cc_final: 0.7149 (tmm) REVERT: J 424 THR cc_start: 0.7799 (OUTLIER) cc_final: 0.7496 (p) REVERT: J 431 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.7987 (pp) outliers start: 93 outliers final: 70 residues processed: 350 average time/residue: 0.3516 time to fit residues: 207.0083 Evaluate side-chains 338 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 258 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 125 HIS Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 261 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 406 HIS Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 226 PHE Chi-restraints excluded: chain I residue 300 VAL Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 411 SER Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 394 THR Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 421 GLU Chi-restraints excluded: chain J residue 424 THR Chi-restraints excluded: chain J residue 431 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 330 optimal weight: 2.9990 chunk 348 optimal weight: 7.9990 chunk 317 optimal weight: 0.9990 chunk 338 optimal weight: 5.9990 chunk 203 optimal weight: 0.8980 chunk 147 optimal weight: 20.0000 chunk 265 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 305 optimal weight: 1.9990 chunk 320 optimal weight: 1.9990 chunk 337 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 158 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 261 HIS D 72 GLN ** D 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 234 GLN H 235 GLN H 238 GLN ** I 200 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 28867 Z= 0.272 Angle : 0.638 12.888 39225 Z= 0.321 Chirality : 0.046 0.164 4657 Planarity : 0.004 0.064 5083 Dihedral : 5.145 56.093 4093 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.81 % Favored : 90.19 % Rotamer: Outliers : 3.26 % Allowed : 25.70 % Favored : 71.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.14), residues: 3771 helix: 0.57 (0.14), residues: 1359 sheet: -2.84 (0.23), residues: 422 loop : -2.46 (0.14), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 37 HIS 0.006 0.001 HIS A 170 PHE 0.024 0.002 PHE E 266 TYR 0.047 0.002 TYR F 94 ARG 0.004 0.000 ARG I 172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 259 time to evaluate : 2.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7741 (tt) REVERT: A 164 MET cc_start: 0.8575 (tpt) cc_final: 0.8263 (tpt) REVERT: A 187 MET cc_start: 0.8199 (tpp) cc_final: 0.7441 (tpp) REVERT: A 208 ASN cc_start: 0.7491 (t0) cc_final: 0.7207 (t0) REVERT: A 287 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.6163 (t0) REVERT: B 14 MET cc_start: 0.7198 (tpp) cc_final: 0.6992 (ttt) REVERT: B 244 GLN cc_start: 0.7511 (tp40) cc_final: 0.7250 (tp40) REVERT: C 34 MET cc_start: 0.7762 (mtm) cc_final: 0.7350 (mtm) REVERT: C 148 MET cc_start: 0.7710 (ttm) cc_final: 0.7297 (tmm) REVERT: C 340 MET cc_start: 0.8095 (tmm) cc_final: 0.7818 (tmm) REVERT: D 226 MET cc_start: 0.8191 (tpt) cc_final: 0.7966 (tpt) REVERT: D 340 MET cc_start: 0.7653 (mmp) cc_final: 0.7321 (mmt) REVERT: E 37 TRP cc_start: 0.7578 (t60) cc_final: 0.7184 (t-100) REVERT: E 44 GLU cc_start: 0.6175 (mm-30) cc_final: 0.5864 (mm-30) REVERT: E 69 MET cc_start: 0.6376 (tmm) cc_final: 0.5805 (tmm) REVERT: E 131 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8299 (tt) REVERT: E 170 MET cc_start: 0.4057 (ppp) cc_final: 0.3474 (ppp) REVERT: F 36 ILE cc_start: 0.6899 (mp) cc_final: 0.6369 (mm) REVERT: F 210 TYR cc_start: 0.7530 (p90) cc_final: 0.4813 (t80) REVERT: F 291 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: G 467 ARG cc_start: 0.6470 (tpm170) cc_final: 0.5315 (tpp-160) REVERT: H 172 ASP cc_start: 0.7341 (t0) cc_final: 0.6966 (t0) REVERT: H 233 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8164 (mt) REVERT: H 499 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8409 (mm) REVERT: J 161 ILE cc_start: 0.9508 (OUTLIER) cc_final: 0.9298 (tt) REVERT: J 173 LYS cc_start: 0.7269 (ptmm) cc_final: 0.6516 (tptp) REVERT: J 224 PHE cc_start: 0.8161 (m-80) cc_final: 0.7339 (m-80) REVERT: J 289 MET cc_start: 0.7718 (tmm) cc_final: 0.7366 (tmm) REVERT: J 424 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7667 (p) REVERT: J 431 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.8084 (pp) outliers start: 93 outliers final: 75 residues processed: 324 average time/residue: 0.3502 time to fit residues: 193.2494 Evaluate side-chains 341 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 257 time to evaluate : 3.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain C residue 301 ASP Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain E residue 292 ASP Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 275 LEU Chi-restraints excluded: chain F residue 291 GLU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 219 VAL Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain H residue 198 ILE Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 230 LEU Chi-restraints excluded: chain H residue 233 LEU Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 406 HIS Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 226 PHE Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 411 SER Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 133 ASP Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 200 ASN Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 421 GLU Chi-restraints excluded: chain J residue 424 THR Chi-restraints excluded: chain J residue 431 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 222 optimal weight: 0.7980 chunk 358 optimal weight: 20.0000 chunk 218 optimal weight: 0.1980 chunk 169 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 375 optimal weight: 0.0040 chunk 345 optimal weight: 9.9990 chunk 299 optimal weight: 0.6980 chunk 31 optimal weight: 0.2980 chunk 231 optimal weight: 0.7980 chunk 183 optimal weight: 30.0000 overall best weight: 0.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN C 158 HIS C 261 HIS ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 235 GLN H 238 GLN ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28867 Z= 0.165 Angle : 0.595 14.960 39225 Z= 0.295 Chirality : 0.044 0.145 4657 Planarity : 0.004 0.064 5083 Dihedral : 4.815 53.705 4093 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 2.84 % Allowed : 26.05 % Favored : 71.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.44 % 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: -1.76 (0.14), residues: 3771 helix: 0.76 (0.15), residues: 1365 sheet: -2.68 (0.23), residues: 443 loop : -2.29 (0.14), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 282 HIS 0.004 0.001 HIS A 170 PHE 0.032 0.001 PHE E 266 TYR 0.017 0.001 TYR E 38 ARG 0.004 0.000 ARG J 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7542 Ramachandran restraints generated. 3771 Oldfield, 0 Emsley, 3771 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 276 time to evaluate : 3.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7432 (tt) REVERT: A 164 MET cc_start: 0.8472 (tpt) cc_final: 0.8247 (tpt) REVERT: A 187 MET cc_start: 0.8091 (tpp) cc_final: 0.7410 (tpp) REVERT: A 208 ASN cc_start: 0.7046 (t0) cc_final: 0.6655 (t0) REVERT: A 287 ASP cc_start: 0.7308 (OUTLIER) cc_final: 0.6129 (t0) REVERT: B 14 MET cc_start: 0.7410 (tpp) cc_final: 0.7110 (ttt) REVERT: B 206 ILE cc_start: 0.8750 (pt) cc_final: 0.8513 (pt) REVERT: B 244 GLN cc_start: 0.7446 (tp40) cc_final: 0.7052 (tp40) REVERT: C 34 MET cc_start: 0.7654 (mtm) cc_final: 0.7336 (mtm) REVERT: C 81 MET cc_start: 0.8360 (mmp) cc_final: 0.7993 (tpp) REVERT: C 148 MET cc_start: 0.7391 (ttm) cc_final: 0.7160 (tmm) REVERT: C 340 MET cc_start: 0.8016 (tmm) cc_final: 0.7740 (tmm) REVERT: D 340 MET cc_start: 0.7119 (mmp) cc_final: 0.6790 (mmt) REVERT: E 37 TRP cc_start: 0.7371 (t60) cc_final: 0.6816 (t-100) REVERT: E 69 MET cc_start: 0.6256 (tmm) cc_final: 0.5768 (tmm) REVERT: E 268 LYS cc_start: 0.6624 (tppt) cc_final: 0.6324 (pttm) REVERT: E 290 TRP cc_start: 0.7091 (t60) cc_final: 0.6778 (p90) REVERT: F 36 ILE cc_start: 0.6848 (mp) cc_final: 0.6318 (mm) REVERT: F 84 MET cc_start: 0.4285 (mtt) cc_final: 0.3835 (mpp) REVERT: F 210 TYR cc_start: 0.7323 (p90) cc_final: 0.4530 (t80) REVERT: G 467 ARG cc_start: 0.6334 (tpm170) cc_final: 0.5186 (tpp-160) REVERT: H 207 MET cc_start: 0.7694 (mmp) cc_final: 0.7490 (mmp) REVERT: H 499 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8233 (mm) REVERT: H 504 LEU cc_start: 0.7630 (mm) cc_final: 0.7183 (tp) REVERT: J 161 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9293 (tt) REVERT: J 173 LYS cc_start: 0.7297 (ptmm) cc_final: 0.6635 (tptp) REVERT: J 224 PHE cc_start: 0.8167 (m-80) cc_final: 0.7444 (m-80) REVERT: J 424 THR cc_start: 0.7733 (OUTLIER) cc_final: 0.7436 (p) REVERT: J 431 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.7931 (pp) outliers start: 81 outliers final: 65 residues processed: 335 average time/residue: 0.3541 time to fit residues: 199.0795 Evaluate side-chains 329 residues out of total 3352 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 258 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 269 GLU Chi-restraints excluded: chain A residue 287 ASP Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 28 ARG Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 113 ASP Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 127 THR Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 150 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 203 ASN Chi-restraints excluded: chain C residue 46 ILE Chi-restraints excluded: chain C residue 60 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 164 VAL Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain D residue 58 MET Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 217 MET Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 289 VAL Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 186 ILE Chi-restraints excluded: chain E residue 272 THR Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 288 ASP Chi-restraints excluded: chain F residue 128 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 394 VAL Chi-restraints excluded: chain H residue 212 LEU Chi-restraints excluded: chain H residue 220 SER Chi-restraints excluded: chain H residue 252 LEU Chi-restraints excluded: chain H residue 287 VAL Chi-restraints excluded: chain H residue 308 VAL Chi-restraints excluded: chain H residue 314 LEU Chi-restraints excluded: chain H residue 359 VAL Chi-restraints excluded: chain H residue 406 HIS Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 499 LEU Chi-restraints excluded: chain H residue 518 VAL Chi-restraints excluded: chain I residue 43 LEU Chi-restraints excluded: chain I residue 150 LEU Chi-restraints excluded: chain I residue 191 SER Chi-restraints excluded: chain I residue 226 PHE Chi-restraints excluded: chain I residue 322 THR Chi-restraints excluded: chain I residue 377 SER Chi-restraints excluded: chain I residue 411 SER Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 67 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 161 ILE Chi-restraints excluded: chain J residue 200 ASN Chi-restraints excluded: chain J residue 236 ASP Chi-restraints excluded: chain J residue 314 ILE Chi-restraints excluded: chain J residue 400 VAL Chi-restraints excluded: chain J residue 421 GLU Chi-restraints excluded: chain J residue 424 THR Chi-restraints excluded: chain J residue 431 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 377 random chunks: chunk 237 optimal weight: 0.9990 chunk 318 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 275 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 299 optimal weight: 7.9990 chunk 125 optimal weight: 4.9990 chunk 307 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 55 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 156 GLN C 261 HIS ** D 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** G 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 455 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.118318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.098513 restraints weight = 61540.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.098506 restraints weight = 60180.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.100180 restraints weight = 51348.541| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 28867 Z= 0.232 Angle : 0.716 59.189 39225 Z= 0.388 Chirality : 0.045 0.528 4657 Planarity : 0.004 0.063 5083 Dihedral : 4.819 53.699 4093 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 2.70 % Allowed : 26.12 % Favored : 71.18 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 5.44 % 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: -1.76 (0.14), residues: 3771 helix: 0.74 (0.15), residues: 1365 sheet: -2.67 (0.23), residues: 443 loop : -2.28 (0.14), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 282 HIS 0.005 0.001 HIS J 290 PHE 0.020 0.001 PHE C 177 TYR 0.016 0.001 TYR E 38 ARG 0.007 0.000 ARG G 428 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5006.47 seconds wall clock time: 93 minutes 2.41 seconds (5582.41 seconds total)