Starting phenix.real_space_refine on Sat Feb 17 04:35:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3x_22036/02_2024/6x3x_22036_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3x_22036/02_2024/6x3x_22036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3x_22036/02_2024/6x3x_22036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3x_22036/02_2024/6x3x_22036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3x_22036/02_2024/6x3x_22036_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3x_22036/02_2024/6x3x_22036_updated.pdb" } resolution = 2.92 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= 0.004 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 S 97 5.16 5 Cl 4 4.86 5 C 11289 2.51 5 N 2837 2.21 5 O 3243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C ARG 318": "NH1" <-> "NH2" Residue "C ARG 321": "NH1" <-> "NH2" Residue "D ARG 17": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D ARG 173": "NH1" <-> "NH2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 176": "NH1" <-> "NH2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E ARG 197": "NH1" <-> "NH2" Residue "E ARG 207": "NH1" <-> "NH2" Residue "E ARG 327": "NH1" <-> "NH2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 104": "OE1" <-> "OE2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "J ARG 102": "NH1" <-> "NH2" Residue "L TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 98": "NH1" <-> "NH2" Residue "K ARG 102": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17470 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2729 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'ABU': 1, 'DZP': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 41 Unusual residues: {'ABU': 1, 'DZP': 1, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'DZP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'DZP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.46, per 1000 atoms: 0.54 Number of scatterers: 17470 At special positions: 0 Unit cell: (145.775, 147.441, 98.294, 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) Cl 4 17.00 S 97 16.00 O 3243 8.00 N 2837 7.00 C 11289 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.06 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 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 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " " MAN G 8 " - " MAN G 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 10 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 404 " - " ASN A 80 " " NAG C 404 " - " ASN C 80 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN D 111 " " NAG N 1 " - " ASN E 208 " Time building additional restraints: 7.11 Conformation dependent library (CDL) restraints added in 3.1 seconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 29 sheets defined 28.3% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 219 through 240 removed outlier: 3.734A pdb=" N LEU A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N MET A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix removed outlier: 4.874A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 269 Processing helix chain 'A' and resid 280 through 308 removed outlier: 4.837A pdb=" N PHE A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N SER A 308 " --> pdb=" O TYR A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 339 Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 224 through 229 removed outlier: 4.051A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 246 removed outlier: 4.177A pdb=" N SER B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N PHE B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TRP B 246 " --> pdb=" O GLN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 273 Processing helix chain 'B' and resid 285 through 310 Processing helix chain 'B' and resid 315 through 343 removed outlier: 3.920A pdb=" N ALA B 319 " --> pdb=" O PRO B 315 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix Processing helix chain 'C' and resid 9 through 19 Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 219 through 241 removed outlier: 5.251A pdb=" N MET C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix removed outlier: 3.867A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 271 removed outlier: 3.629A pdb=" N GLU C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR C 271 " --> pdb=" O HIS C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 304 Processing helix chain 'C' and resid 310 through 338 removed outlier: 3.591A pdb=" N ILE C 322 " --> pdb=" O ARG C 318 " (cutoff:3.500A) Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 224 through 229 removed outlier: 3.765A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 246 removed outlier: 4.118A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TRP D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 274 Processing helix chain 'D' and resid 285 through 310 Processing helix chain 'D' and resid 315 through 345 removed outlier: 3.712A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N PHE D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Proline residue: D 330 - end of helix Processing helix chain 'E' and resid 26 through 34 Processing helix chain 'E' and resid 100 through 105 removed outlier: 3.525A pdb=" N VAL E 103 " --> pdb=" O SER E 100 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 255 removed outlier: 5.679A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix removed outlier: 4.155A pdb=" N SER E 254 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N PHE E 255 " --> pdb=" O SER E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 283 Processing helix chain 'E' and resid 297 through 323 removed outlier: 3.957A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 356 removed outlier: 4.974A pdb=" N LYS E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N MET E 331 " --> pdb=" O ARG E 327 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ASP E 332 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) Proline residue: E 340 - end of helix Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'A' and resid 164 through 168 removed outlier: 6.328A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.675A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.763A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 167 through 171 removed outlier: 6.176A pdb=" N THR B 39 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N GLU B 170 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL B 41 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 45 through 47 Processing sheet with id= F, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.241A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N LEU B 193 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.361A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU C 83 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.919A pdb=" N MET C 49 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.612A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.669A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 167 through 171 removed outlier: 6.322A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 45 through 47 Processing sheet with id= M, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= N, first strand: chain 'D' and resid 150 through 154 removed outlier: 3.958A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 179 through 183 removed outlier: 5.870A pdb=" N THR E 51 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N GLN E 182 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N ILE E 53 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 188 through 190 removed outlier: 6.700A pdb=" N MET E 57 " --> pdb=" O GLU E 189 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.683A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 116 through 121 removed outlier: 7.010A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 4 through 7 Processing sheet with id= T, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.506A pdb=" N LYS I 102 " --> pdb=" O MET I 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'I' and resid 85 through 90 removed outlier: 6.301A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 3 through 6 Processing sheet with id= W, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.523A pdb=" N ALA J 92 " --> pdb=" O VAL J 114 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N LYS J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N TRP J 47 " --> pdb=" O LYS J 38 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= Y, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.582A pdb=" N LYS L 102 " --> pdb=" O MET L 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'L' and resid 85 through 90 removed outlier: 6.267A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'K' and resid 3 through 6 Processing sheet with id= AB, first strand: chain 'K' and resid 10 through 12 Processing sheet with id= AC, first strand: chain 'K' and resid 58 through 60 removed outlier: 6.911A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N TYR K 33 " --> pdb=" O LYS K 99 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 737 hydrogen bonds defined for protein. 2151 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: 5.26 Time building geometry restraints manager: 7.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 4970 1.34 - 1.47: 5180 1.47 - 1.60: 7584 1.60 - 1.73: 7 1.73 - 1.87: 171 Bond restraints: 17912 Sorted by residual: bond pdb=" C5 DZP A 406 " pdb=" N15 DZP A 406 " ideal model delta sigma weight residual 1.272 1.517 -0.245 2.00e-02 2.50e+03 1.49e+02 bond pdb=" C5 DZP C 406 " pdb=" N15 DZP C 406 " ideal model delta sigma weight residual 1.272 1.515 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" C5 DZP D 404 " pdb=" N15 DZP D 404 " ideal model delta sigma weight residual 1.272 1.513 -0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C5 DZP E 403 " pdb=" N15 DZP E 403 " ideal model delta sigma weight residual 1.272 1.512 -0.240 2.00e-02 2.50e+03 1.44e+02 bond pdb=" C18 DZP E 403 " pdb=" N2 DZP E 403 " ideal model delta sigma weight residual 1.368 1.523 -0.155 2.00e-02 2.50e+03 6.01e+01 ... (remaining 17907 not shown) Histogram of bond angle deviations from ideal: 97.26 - 105.33: 363 105.33 - 113.39: 9798 113.39 - 121.46: 9643 121.46 - 129.53: 4413 129.53 - 137.60: 145 Bond angle restraints: 24362 Sorted by residual: angle pdb=" CA GLU J 42 " pdb=" CB GLU J 42 " pdb=" CG GLU J 42 " ideal model delta sigma weight residual 114.10 126.14 -12.04 2.00e+00 2.50e-01 3.62e+01 angle pdb=" CA LEU E 287 " pdb=" CB LEU E 287 " pdb=" CG LEU E 287 " ideal model delta sigma weight residual 116.30 136.40 -20.10 3.50e+00 8.16e-02 3.30e+01 angle pdb=" C CYS A 150 " pdb=" CA CYS A 150 " pdb=" CB CYS A 150 " ideal model delta sigma weight residual 109.71 120.22 -10.51 1.83e+00 2.99e-01 3.30e+01 angle pdb=" CA LYS B 78 " pdb=" CB LYS B 78 " pdb=" CG LYS B 78 " ideal model delta sigma weight residual 114.10 125.05 -10.95 2.00e+00 2.50e-01 3.00e+01 angle pdb=" C GLY C 170 " pdb=" N ASP C 171 " pdb=" CA ASP C 171 " ideal model delta sigma weight residual 121.54 130.90 -9.36 1.91e+00 2.74e-01 2.40e+01 ... (remaining 24357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.47: 10494 29.47 - 58.93: 288 58.93 - 88.40: 56 88.40 - 117.86: 27 117.86 - 147.33: 11 Dihedral angle restraints: 10876 sinusoidal: 4620 harmonic: 6256 Sorted by residual: dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 165 " pdb=" CB CYS E 165 " ideal model delta sinusoidal sigma weight residual -86.00 -13.37 -72.63 1 1.00e+01 1.00e-02 6.73e+01 dihedral pdb=" CA VAL D 64 " pdb=" C VAL D 64 " pdb=" N PHE D 65 " pdb=" CA PHE D 65 " ideal model delta harmonic sigma weight residual 180.00 154.63 25.37 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA CYS E 165 " pdb=" C CYS E 165 " pdb=" N PRO E 166 " pdb=" CA PRO E 166 " ideal model delta harmonic sigma weight residual 180.00 -155.27 -24.73 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 10873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.913: 2799 0.913 - 1.825: 6 1.825 - 2.738: 0 2.738 - 3.650: 0 3.650 - 4.563: 2 Chirality restraints: 2807 Sorted by residual: chirality pdb=" C1 MAN G 4 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 1.12 1.28 2.00e-02 2.50e+03 4.10e+03 chirality pdb=" C1 MAN G 10 " pdb=" O3 MAN G 7 " pdb=" C2 MAN G 10 " pdb=" O5 MAN G 10 " both_signs ideal model delta sigma weight residual False 2.40 1.24 1.16 2.00e-02 2.50e+03 3.36e+03 chirality pdb=" C1 MAN G 5 " pdb=" O2 MAN G 4 " pdb=" C2 MAN G 5 " pdb=" O5 MAN G 5 " both_signs ideal model delta sigma weight residual False 2.40 1.27 1.13 2.00e-02 2.50e+03 3.19e+03 ... (remaining 2804 not shown) Planarity restraints: 3001 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 1 " 0.155 2.00e-02 2.50e+03 1.32e-01 2.17e+02 pdb=" C7 NAG F 1 " -0.038 2.00e-02 2.50e+03 pdb=" C8 NAG F 1 " 0.111 2.00e-02 2.50e+03 pdb=" N2 NAG F 1 " -0.221 2.00e-02 2.50e+03 pdb=" O7 NAG F 1 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.147 2.00e-02 2.50e+03 1.22e-01 1.85e+02 pdb=" C7 NAG F 2 " 0.040 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.110 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.195 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " -0.077 2.00e-02 2.50e+03 6.30e-02 4.96e+01 pdb=" C7 NAG H 2 " 0.021 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " -0.058 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " 0.099 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " 0.015 2.00e-02 2.50e+03 ... (remaining 2998 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 3075 2.77 - 3.30: 15053 3.30 - 3.84: 29367 3.84 - 4.37: 35371 4.37 - 4.90: 62321 Nonbonded interactions: 145187 Sorted by model distance: nonbonded pdb=" OG SER L 67 " pdb=" O ASP L 70 " model vdw 2.241 2.440 nonbonded pdb=" O ALA E 295 " pdb=" OH TYR E 350 " model vdw 2.255 2.440 nonbonded pdb=" OD2 ASP K 73 " pdb=" OG SER K 76 " model vdw 2.269 2.440 nonbonded pdb=" ND2 ASN C 243 " pdb=" OD2 ASP C 245 " model vdw 2.293 2.520 nonbonded pdb=" O VAL B 257 " pdb=" OG1 THR B 261 " model vdw 2.299 2.440 ... (remaining 145182 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 10 through 347) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 1 through 105) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 2 through 117) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.010 Extract box with map and model: 5.890 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 48.000 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.140 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: 0.000 Load rotamer database and sin/cos tables:11.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 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 : 0.010 0.245 17912 Z= 0.609 Angle : 1.110 20.098 24362 Z= 0.577 Chirality : 0.146 4.563 2807 Planarity : 0.007 0.132 2994 Dihedral : 16.355 147.328 6829 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.58 % Allowed : 4.94 % Favored : 94.48 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -2.15 (0.16), residues: 2103 helix: -0.61 (0.19), residues: 584 sheet: -0.90 (0.19), residues: 615 loop : -2.33 (0.17), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 241 HIS 0.004 0.001 HIS E 156 PHE 0.052 0.004 PHE B 258 TYR 0.027 0.003 TYR C 157 ARG 0.006 0.001 ARG D 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 487 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 ASP cc_start: 0.7643 (t70) cc_final: 0.7400 (t70) REVERT: A 231 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7691 (mp) REVERT: A 319 TRP cc_start: 0.7387 (t60) cc_final: 0.7180 (t60) REVERT: B 20 ASP cc_start: 0.7792 (m-30) cc_final: 0.7495 (m-30) REVERT: B 138 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7589 (mt-10) REVERT: B 156 LYS cc_start: 0.8636 (mtmm) cc_final: 0.8274 (mtpt) REVERT: C 41 ASN cc_start: 0.8035 (m110) cc_final: 0.7781 (m-40) REVERT: C 215 LYS cc_start: 0.8415 (ttpp) cc_final: 0.8035 (tptt) REVERT: C 294 MET cc_start: 0.6428 (ptt) cc_final: 0.6084 (ptt) REVERT: D 83 VAL cc_start: 0.9067 (p) cc_final: 0.8826 (t) REVERT: D 126 THR cc_start: 0.8624 (t) cc_final: 0.8323 (m) REVERT: J 80 TYR cc_start: 0.8262 (m-80) cc_final: 0.7998 (m-80) REVERT: J 87 THR cc_start: 0.8599 (t) cc_final: 0.8390 (p) REVERT: L 72 THR cc_start: 0.8776 (m) cc_final: 0.8555 (p) outliers start: 11 outliers final: 7 residues processed: 496 average time/residue: 1.3565 time to fit residues: 744.9236 Evaluate side-chains 348 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 340 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.0470 chunk 156 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 105 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 162 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 187 optimal weight: 7.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 65 GLN A 113 ASN A 224 GLN B 68 GLN B 189 ASN B 229 GLN B 242 GLN B 346 ASN C 65 GLN C 85 ASN C 148 GLN C 332 ASN D 68 GLN E 80 GLN E 90 ASN E 128 ASN J 6 GLN J 110 GLN L 42 GLN K 5 GLN K 6 GLN K 43 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17912 Z= 0.162 Angle : 0.619 13.235 24362 Z= 0.304 Chirality : 0.051 1.031 2807 Planarity : 0.004 0.042 2994 Dihedral : 14.313 149.689 2902 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.61 % Allowed : 15.61 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % 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: -1.00 (0.17), residues: 2103 helix: 0.76 (0.21), residues: 569 sheet: -0.56 (0.19), residues: 676 loop : -1.67 (0.19), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 103 HIS 0.003 0.001 HIS D 216 PHE 0.017 0.001 PHE B 258 TYR 0.030 0.001 TYR C 299 ARG 0.008 0.000 ARG K 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 349 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 163 ASP cc_start: 0.7828 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: A 227 MET cc_start: 0.6256 (mmp) cc_final: 0.6048 (mmt) REVERT: A 298 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8652 (tm-30) REVERT: A 318 ARG cc_start: 0.6842 (mtp-110) cc_final: 0.6298 (ppt170) REVERT: B 20 ASP cc_start: 0.7754 (m-30) cc_final: 0.7418 (m-30) REVERT: B 138 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7799 (mt-10) REVERT: B 156 LYS cc_start: 0.8559 (mtmm) cc_final: 0.8222 (mtpt) REVERT: B 236 MET cc_start: 0.7567 (mmt) cc_final: 0.7339 (mmp) REVERT: B 301 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7656 (tt) REVERT: C 40 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.7110 (mpt) REVERT: C 243 ASN cc_start: 0.6787 (t0) cc_final: 0.6264 (t0) REVERT: C 245 ASP cc_start: 0.7193 (p0) cc_final: 0.6992 (m-30) REVERT: D 83 VAL cc_start: 0.9226 (p) cc_final: 0.8826 (t) REVERT: D 338 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8263 (tp) REVERT: E 154 GLN cc_start: 0.7983 (mm110) cc_final: 0.7721 (tp40) REVERT: E 168 GLU cc_start: 0.7975 (mt-10) cc_final: 0.7716 (mt-10) REVERT: E 189 GLU cc_start: 0.7343 (OUTLIER) cc_final: 0.6924 (mt-10) REVERT: E 211 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6133 (mp0) REVERT: E 334 TYR cc_start: 0.7828 (m-10) cc_final: 0.7602 (m-10) REVERT: J 80 TYR cc_start: 0.8334 (m-80) cc_final: 0.8024 (m-80) REVERT: J 82 GLN cc_start: 0.8301 (tt0) cc_final: 0.7704 (tp40) REVERT: J 84 SER cc_start: 0.7551 (p) cc_final: 0.7300 (m) outliers start: 68 outliers final: 26 residues processed: 379 average time/residue: 1.2456 time to fit residues: 528.6561 Evaluate side-chains 353 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 320 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 349 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain K residue 71 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 chunk 128 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 188 optimal weight: 3.9990 chunk 203 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 186 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 229 GLN C 41 ASN C 332 ASN D 102 HIS ** D 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 110 GLN K 5 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 17912 Z= 0.432 Angle : 0.721 11.845 24362 Z= 0.358 Chirality : 0.055 1.194 2807 Planarity : 0.005 0.052 2994 Dihedral : 13.728 149.593 2891 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 5.74 % Allowed : 15.67 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.17), residues: 2103 helix: 0.89 (0.21), residues: 589 sheet: -0.24 (0.19), residues: 649 loop : -1.34 (0.19), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 241 HIS 0.009 0.001 HIS D 102 PHE 0.023 0.002 PHE E 236 TYR 0.028 0.002 TYR C 299 ARG 0.005 0.001 ARG B 323 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 335 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.8362 (OUTLIER) cc_final: 0.7756 (tmtt) REVERT: A 298 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8678 (tm-30) REVERT: A 318 ARG cc_start: 0.7001 (mtp-110) cc_final: 0.6338 (ppt170) REVERT: B 138 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7894 (mt-10) REVERT: B 156 LYS cc_start: 0.8639 (mtmm) cc_final: 0.8316 (mtpt) REVERT: B 236 MET cc_start: 0.7577 (mmt) cc_final: 0.7254 (mmp) REVERT: B 301 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7634 (tt) REVERT: B 327 ILE cc_start: 0.8256 (mt) cc_final: 0.7927 (mm) REVERT: B 338 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8055 (tm) REVERT: C 243 ASN cc_start: 0.6895 (t0) cc_final: 0.6412 (t0) REVERT: C 245 ASP cc_start: 0.7387 (p0) cc_final: 0.7125 (m-30) REVERT: C 286 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.7006 (mtm) REVERT: D 338 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8345 (tt) REVERT: E 189 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.6941 (mt-10) REVERT: E 211 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6620 (mp0) REVERT: J 52 ASP cc_start: 0.8208 (t0) cc_final: 0.7981 (t0) REVERT: J 80 TYR cc_start: 0.8454 (m-80) cc_final: 0.8111 (m-80) REVERT: J 82 GLN cc_start: 0.8374 (tt0) cc_final: 0.7791 (tp40) outliers start: 108 outliers final: 55 residues processed: 388 average time/residue: 1.3042 time to fit residues: 565.0334 Evaluate side-chains 379 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 316 time to evaluate : 1.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 41 ASN Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 91 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 188 optimal weight: 0.0170 chunk 200 optimal weight: 0.8980 chunk 98 optimal weight: 8.9990 chunk 179 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 189 ASN B 229 GLN C 41 ASN D 151 HIS D 190 GLN E 69 ASN E 90 ASN E 163 HIS ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 110 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17912 Z= 0.168 Angle : 0.566 9.401 24362 Z= 0.282 Chirality : 0.047 1.009 2807 Planarity : 0.004 0.037 2994 Dihedral : 13.104 155.116 2891 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.62 % Allowed : 18.00 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2103 helix: 1.54 (0.22), residues: 565 sheet: -0.13 (0.19), residues: 660 loop : -1.07 (0.20), residues: 878 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 103 HIS 0.002 0.001 HIS D 216 PHE 0.012 0.001 PHE B 258 TYR 0.029 0.001 TYR C 299 ARG 0.007 0.000 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 327 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 148 GLN cc_start: 0.8338 (OUTLIER) cc_final: 0.7026 (mm-40) REVERT: A 274 LYS cc_start: 0.8400 (mttt) cc_final: 0.8144 (mttm) REVERT: A 298 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8602 (tm-30) REVERT: A 318 ARG cc_start: 0.6958 (mtp-110) cc_final: 0.6364 (ppt170) REVERT: B 138 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7892 (mt-10) REVERT: B 156 LYS cc_start: 0.8609 (mtmm) cc_final: 0.8206 (mtpt) REVERT: B 236 MET cc_start: 0.7540 (mmt) cc_final: 0.7152 (mmp) REVERT: B 258 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.5739 (t80) REVERT: B 301 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7610 (tt) REVERT: B 327 ILE cc_start: 0.8234 (mt) cc_final: 0.7936 (mm) REVERT: C 243 ASN cc_start: 0.6974 (t0) cc_final: 0.6316 (t0) REVERT: C 245 ASP cc_start: 0.7383 (p0) cc_final: 0.7054 (m-30) REVERT: C 318 ARG cc_start: 0.7551 (mtp85) cc_final: 0.7227 (mtt-85) REVERT: D 17 ARG cc_start: 0.7488 (mtm-85) cc_final: 0.7237 (mtm110) REVERT: D 83 VAL cc_start: 0.9236 (OUTLIER) cc_final: 0.8686 (t) REVERT: D 138 GLU cc_start: 0.7368 (tt0) cc_final: 0.7040 (tp30) REVERT: D 213 MET cc_start: 0.8521 (mmm) cc_final: 0.7993 (mtm) REVERT: D 246 TRP cc_start: 0.8771 (m100) cc_final: 0.8471 (m-90) REVERT: E 189 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.6981 (mt-10) REVERT: J 52 ASP cc_start: 0.8061 (t0) cc_final: 0.7822 (t0) REVERT: J 82 GLN cc_start: 0.8281 (tt0) cc_final: 0.7783 (tp40) outliers start: 87 outliers final: 46 residues processed: 366 average time/residue: 1.2686 time to fit residues: 518.0865 Evaluate side-chains 364 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 312 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 225 THR Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain D residue 71 LYS Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain K residue 71 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 82 optimal weight: 0.7980 chunk 170 optimal weight: 0.9980 chunk 138 optimal weight: 0.0770 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 2.9990 chunk 179 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 229 GLN C 41 ASN C 332 ASN E 69 ASN E 90 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17912 Z= 0.150 Angle : 0.540 9.363 24362 Z= 0.267 Chirality : 0.042 0.214 2807 Planarity : 0.004 0.038 2994 Dihedral : 12.651 156.276 2891 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.57 % Allowed : 19.49 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.18), residues: 2103 helix: 1.80 (0.22), residues: 565 sheet: -0.12 (0.19), residues: 682 loop : -0.83 (0.21), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 103 HIS 0.002 0.000 HIS D 216 PHE 0.012 0.001 PHE B 258 TYR 0.025 0.001 TYR C 299 ARG 0.009 0.000 ARG B 323 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 324 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8765 (OUTLIER) cc_final: 0.7552 (mpt) REVERT: A 49 MET cc_start: 0.5030 (pp-130) cc_final: 0.4800 (pp-130) REVERT: A 148 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.6749 (mm-40) REVERT: A 163 ASP cc_start: 0.8294 (m-30) cc_final: 0.8064 (m-30) REVERT: A 196 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8127 (pttm) REVERT: A 274 LYS cc_start: 0.8424 (mttt) cc_final: 0.8157 (mttm) REVERT: A 298 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.8605 (tm-30) REVERT: A 318 ARG cc_start: 0.6969 (mtp-110) cc_final: 0.6386 (ppt170) REVERT: B 138 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7875 (mt-10) REVERT: B 156 LYS cc_start: 0.8572 (mtmm) cc_final: 0.8188 (mtpt) REVERT: B 236 MET cc_start: 0.7560 (mmt) cc_final: 0.7167 (mmp) REVERT: B 258 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.5649 (t80) REVERT: B 301 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7604 (tt) REVERT: B 327 ILE cc_start: 0.8184 (mt) cc_final: 0.7902 (mm) REVERT: C 243 ASN cc_start: 0.6954 (t0) cc_final: 0.6238 (t0) REVERT: C 245 ASP cc_start: 0.7388 (p0) cc_final: 0.7088 (m-30) REVERT: C 318 ARG cc_start: 0.7455 (mtp85) cc_final: 0.7118 (mtt-85) REVERT: D 138 GLU cc_start: 0.7379 (tt0) cc_final: 0.7076 (tp30) REVERT: D 246 TRP cc_start: 0.8762 (m100) cc_final: 0.8467 (m-90) REVERT: D 338 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8273 (tp) REVERT: E 189 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.6973 (mt-10) REVERT: J 52 ASP cc_start: 0.8028 (t0) cc_final: 0.7801 (t0) REVERT: J 82 GLN cc_start: 0.8256 (tt0) cc_final: 0.7749 (tp40) REVERT: L 104 GLU cc_start: 0.3726 (OUTLIER) cc_final: 0.3277 (mt-10) REVERT: K 90 ASP cc_start: 0.7490 (m-30) cc_final: 0.6739 (p0) outliers start: 86 outliers final: 52 residues processed: 365 average time/residue: 1.2736 time to fit residues: 519.0826 Evaluate side-chains 380 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 319 time to evaluate : 1.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 148 GLN Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 298 GLU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain J residue 67 LYS Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain K residue 71 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 2.9990 chunk 180 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 166 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 229 GLN C 41 ASN C 224 GLN D 248 ASN E 69 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 258 ASN J 3 GLN J 110 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.062 17912 Z= 0.502 Angle : 0.717 11.042 24362 Z= 0.358 Chirality : 0.049 0.332 2807 Planarity : 0.005 0.066 2994 Dihedral : 13.060 148.122 2891 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.68 % Allowed : 19.28 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.18), residues: 2103 helix: 1.37 (0.22), residues: 575 sheet: -0.12 (0.19), residues: 675 loop : -0.86 (0.21), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 241 HIS 0.006 0.001 HIS D 102 PHE 0.025 0.002 PHE E 236 TYR 0.024 0.002 TYR C 157 ARG 0.007 0.001 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 318 time to evaluate : 2.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.7668 (mpt) REVERT: A 274 LYS cc_start: 0.8521 (mttt) cc_final: 0.8241 (mttm) REVERT: A 318 ARG cc_start: 0.7047 (mtp-110) cc_final: 0.6456 (ppt170) REVERT: B 78 LYS cc_start: 0.8262 (mmpt) cc_final: 0.7760 (mptt) REVERT: B 138 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7947 (mt-10) REVERT: B 236 MET cc_start: 0.7544 (mmt) cc_final: 0.7219 (mmp) REVERT: B 258 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.5537 (t80) REVERT: B 301 LEU cc_start: 0.7998 (OUTLIER) cc_final: 0.7614 (tt) REVERT: B 327 ILE cc_start: 0.8230 (mt) cc_final: 0.7924 (mm) REVERT: C 64 GLN cc_start: 0.8656 (mt0) cc_final: 0.8395 (mp10) REVERT: C 243 ASN cc_start: 0.7035 (t0) cc_final: 0.6358 (t0) REVERT: C 245 ASP cc_start: 0.7507 (p0) cc_final: 0.7152 (m-30) REVERT: C 318 ARG cc_start: 0.7484 (mtp85) cc_final: 0.7185 (mtt-85) REVERT: D 17 ARG cc_start: 0.7468 (mtm-85) cc_final: 0.7242 (mtm110) REVERT: D 338 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8364 (tt) REVERT: E 85 ARG cc_start: 0.7215 (OUTLIER) cc_final: 0.7001 (ptm160) REVERT: E 94 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.8015 (mmpt) REVERT: E 189 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6935 (mt-10) REVERT: E 211 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6747 (mp0) REVERT: J 3 GLN cc_start: 0.7755 (OUTLIER) cc_final: 0.7527 (tm-30) REVERT: J 52 ASP cc_start: 0.8220 (t0) cc_final: 0.7996 (t0) REVERT: J 80 TYR cc_start: 0.8533 (m-80) cc_final: 0.8192 (m-80) REVERT: J 82 GLN cc_start: 0.8328 (tt0) cc_final: 0.7783 (tp40) REVERT: L 104 GLU cc_start: 0.3764 (OUTLIER) cc_final: 0.3090 (mt-10) outliers start: 107 outliers final: 70 residues processed: 371 average time/residue: 1.2566 time to fit residues: 520.3674 Evaluate side-chains 382 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 302 time to evaluate : 2.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 285 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 150 CYS Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 85 ARG Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 297 ASP Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 317 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain L residue 13 MET Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain K residue 12 VAL Chi-restraints excluded: chain K residue 71 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 114 optimal weight: 0.4980 chunk 146 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 168 optimal weight: 0.6980 chunk 111 optimal weight: 0.8980 chunk 199 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 121 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 189 ASN B 229 GLN B 248 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 303 ASN E 90 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 17912 Z= 0.160 Angle : 0.557 8.114 24362 Z= 0.278 Chirality : 0.042 0.215 2807 Planarity : 0.004 0.044 2994 Dihedral : 12.617 154.865 2891 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.72 % Allowed : 21.99 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.18), residues: 2103 helix: 1.83 (0.22), residues: 567 sheet: -0.04 (0.19), residues: 670 loop : -0.65 (0.21), residues: 866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 241 HIS 0.002 0.000 HIS D 216 PHE 0.013 0.001 PHE B 258 TYR 0.033 0.001 TYR A 299 ARG 0.013 0.000 ARG B 323 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 312 time to evaluate : 1.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.7510 (mpt) REVERT: A 196 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8127 (pttp) REVERT: A 274 LYS cc_start: 0.8503 (mttt) cc_final: 0.8219 (mttm) REVERT: A 318 ARG cc_start: 0.6980 (mtp-110) cc_final: 0.6456 (ppt170) REVERT: B 138 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7906 (mt-10) REVERT: B 236 MET cc_start: 0.7516 (mmt) cc_final: 0.7136 (mmp) REVERT: B 258 PHE cc_start: 0.7356 (OUTLIER) cc_final: 0.5504 (t80) REVERT: B 301 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7607 (tt) REVERT: B 327 ILE cc_start: 0.8223 (mt) cc_final: 0.7964 (mm) REVERT: C 21 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7532 (ttpt) REVERT: C 64 GLN cc_start: 0.8607 (mt0) cc_final: 0.8385 (mp10) REVERT: C 318 ARG cc_start: 0.7502 (mtp85) cc_final: 0.7139 (mtt-85) REVERT: D 17 ARG cc_start: 0.7487 (mtm-85) cc_final: 0.7252 (mtm110) REVERT: D 213 MET cc_start: 0.8432 (mmm) cc_final: 0.8084 (mtm) REVERT: D 246 TRP cc_start: 0.8792 (m100) cc_final: 0.8486 (m-90) REVERT: E 85 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6946 (ptm160) REVERT: E 94 LYS cc_start: 0.8175 (mmtp) cc_final: 0.7919 (mmpt) REVERT: E 211 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6582 (mp0) REVERT: J 52 ASP cc_start: 0.8067 (t0) cc_final: 0.7856 (t0) REVERT: J 82 GLN cc_start: 0.8283 (tt0) cc_final: 0.7766 (tp40) REVERT: L 13 MET cc_start: 0.7095 (OUTLIER) cc_final: 0.6871 (ppp) REVERT: L 104 GLU cc_start: 0.3803 (OUTLIER) cc_final: 0.3198 (mt-10) outliers start: 70 outliers final: 45 residues processed: 346 average time/residue: 1.3365 time to fit residues: 519.8365 Evaluate side-chains 361 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 307 time to evaluate : 1.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 85 ARG Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain L residue 13 MET Chi-restraints excluded: chain L residue 34 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 71 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 119 optimal weight: 5.9990 chunk 60 optimal weight: 0.0470 chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 135 optimal weight: 0.0980 chunk 98 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 156 optimal weight: 2.9990 overall best weight: 0.5480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 ASN B 229 GLN B 248 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 332 ASN ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 17912 Z= 0.149 Angle : 0.537 7.000 24362 Z= 0.267 Chirality : 0.042 0.198 2807 Planarity : 0.004 0.040 2994 Dihedral : 12.341 156.570 2891 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.56 % Allowed : 22.46 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.19), residues: 2103 helix: 2.01 (0.22), residues: 567 sheet: 0.05 (0.19), residues: 665 loop : -0.50 (0.22), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 351 HIS 0.002 0.000 HIS D 216 PHE 0.012 0.001 PHE B 258 TYR 0.025 0.001 TYR C 299 ARG 0.015 0.000 ARG K 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 318 time to evaluate : 2.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.7437 (mpt) REVERT: A 196 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8095 (pttp) REVERT: A 274 LYS cc_start: 0.8521 (mttt) cc_final: 0.8231 (mttm) REVERT: A 318 ARG cc_start: 0.6948 (mtp-110) cc_final: 0.6377 (ppt170) REVERT: B 138 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7920 (mt-10) REVERT: B 236 MET cc_start: 0.7527 (mmt) cc_final: 0.7045 (mmp) REVERT: B 258 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.5662 (t80) REVERT: B 301 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7581 (tt) REVERT: B 327 ILE cc_start: 0.8213 (mt) cc_final: 0.7943 (mm) REVERT: C 21 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7422 (ttpt) REVERT: C 185 GLN cc_start: 0.8159 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: C 243 ASN cc_start: 0.7045 (t0) cc_final: 0.6542 (t0) REVERT: C 245 ASP cc_start: 0.7523 (p0) cc_final: 0.7246 (m-30) REVERT: D 17 ARG cc_start: 0.7465 (mtm-85) cc_final: 0.7231 (mtm110) REVERT: D 138 GLU cc_start: 0.7377 (tt0) cc_final: 0.7092 (tp30) REVERT: D 213 MET cc_start: 0.8429 (mmm) cc_final: 0.8057 (mtm) REVERT: D 246 TRP cc_start: 0.8753 (m100) cc_final: 0.8474 (m-90) REVERT: E 85 ARG cc_start: 0.7172 (OUTLIER) cc_final: 0.6970 (ptm160) REVERT: E 94 LYS cc_start: 0.8158 (mmtp) cc_final: 0.7935 (mmpt) REVERT: E 305 ILE cc_start: 0.8719 (OUTLIER) cc_final: 0.8497 (mp) REVERT: J 3 GLN cc_start: 0.7757 (tm-30) cc_final: 0.7484 (pp30) REVERT: J 82 GLN cc_start: 0.8275 (tt0) cc_final: 0.7755 (tp40) REVERT: L 13 MET cc_start: 0.7031 (OUTLIER) cc_final: 0.6823 (ppp) REVERT: L 104 GLU cc_start: 0.3841 (OUTLIER) cc_final: 0.3220 (mt-10) REVERT: K 40 ARG cc_start: 0.7612 (mtt90) cc_final: 0.7405 (mpt-90) REVERT: K 90 ASP cc_start: 0.7543 (m-30) cc_final: 0.6838 (p0) outliers start: 67 outliers final: 45 residues processed: 353 average time/residue: 1.2471 time to fit residues: 491.8723 Evaluate side-chains 366 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 311 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 196 LYS Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 63 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 302 VAL Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 85 ARG Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain L residue 13 MET Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 71 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 0.0470 chunk 191 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 111 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 145 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 168 optimal weight: 4.9990 chunk 175 optimal weight: 0.0570 chunk 122 optimal weight: 5.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 189 ASN B 229 GLN B 248 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN K 5 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 17912 Z= 0.163 Angle : 0.539 7.172 24362 Z= 0.267 Chirality : 0.042 0.201 2807 Planarity : 0.004 0.042 2994 Dihedral : 12.215 156.400 2889 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.77 % Allowed : 22.57 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.19), residues: 2103 helix: 2.03 (0.22), residues: 567 sheet: 0.11 (0.19), residues: 664 loop : -0.42 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 241 HIS 0.002 0.000 HIS D 216 PHE 0.012 0.001 PHE B 258 TYR 0.024 0.001 TYR C 299 ARG 0.009 0.000 ARG K 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 315 time to evaluate : 2.085 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.7466 (mpt) REVERT: A 274 LYS cc_start: 0.8528 (mttt) cc_final: 0.8238 (mttm) REVERT: A 318 ARG cc_start: 0.6940 (mtp-110) cc_final: 0.6369 (ppt170) REVERT: B 138 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7919 (mt-10) REVERT: B 236 MET cc_start: 0.7519 (mmt) cc_final: 0.7035 (mmp) REVERT: B 258 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.5655 (t80) REVERT: B 301 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7568 (tt) REVERT: B 327 ILE cc_start: 0.8206 (mt) cc_final: 0.7941 (mm) REVERT: C 21 LYS cc_start: 0.7678 (OUTLIER) cc_final: 0.7424 (ttpt) REVERT: C 185 GLN cc_start: 0.8115 (OUTLIER) cc_final: 0.7810 (tt0) REVERT: C 243 ASN cc_start: 0.7029 (t0) cc_final: 0.6557 (t0) REVERT: C 245 ASP cc_start: 0.7428 (p0) cc_final: 0.7206 (m-30) REVERT: D 17 ARG cc_start: 0.7470 (mtm-85) cc_final: 0.7239 (mtm110) REVERT: D 138 GLU cc_start: 0.7373 (tt0) cc_final: 0.7086 (tp30) REVERT: D 213 MET cc_start: 0.8454 (mmm) cc_final: 0.8036 (mtm) REVERT: D 246 TRP cc_start: 0.8770 (m100) cc_final: 0.8489 (m-90) REVERT: E 85 ARG cc_start: 0.7174 (OUTLIER) cc_final: 0.6968 (ptm160) REVERT: E 94 LYS cc_start: 0.8137 (mmtp) cc_final: 0.7908 (mmpt) REVERT: E 148 ASP cc_start: 0.7824 (t70) cc_final: 0.7602 (t70) REVERT: E 305 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8501 (mp) REVERT: J 82 GLN cc_start: 0.8275 (tt0) cc_final: 0.7754 (tp40) REVERT: L 104 GLU cc_start: 0.3941 (OUTLIER) cc_final: 0.3308 (mt-10) REVERT: K 90 ASP cc_start: 0.7472 (m-30) cc_final: 0.6881 (p0) outliers start: 71 outliers final: 45 residues processed: 349 average time/residue: 1.2855 time to fit residues: 500.4204 Evaluate side-chains 364 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 311 time to evaluate : 2.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 73 THR Chi-restraints excluded: chain E residue 85 ARG Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 6.9990 chunk 119 optimal weight: 0.2980 chunk 93 optimal weight: 0.9980 chunk 136 optimal weight: 0.9990 chunk 206 optimal weight: 5.9990 chunk 189 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 17 optimal weight: 0.0570 chunk 126 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 overall best weight: 1.0702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 189 ASN B 229 GLN B 248 ASN C 41 ASN ** D 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 110 GLN K 5 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 17912 Z= 0.196 Angle : 0.562 7.284 24362 Z= 0.279 Chirality : 0.043 0.302 2807 Planarity : 0.004 0.037 2994 Dihedral : 12.214 156.079 2889 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.51 % Allowed : 22.68 % Favored : 73.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 2103 helix: 2.01 (0.22), residues: 567 sheet: 0.05 (0.19), residues: 676 loop : -0.34 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 241 HIS 0.002 0.001 HIS D 102 PHE 0.013 0.001 PHE E 236 TYR 0.023 0.001 TYR C 299 ARG 0.008 0.000 ARG B 323 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 309 time to evaluate : 2.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.7499 (mpt) REVERT: A 274 LYS cc_start: 0.8537 (mttt) cc_final: 0.8255 (mttm) REVERT: A 318 ARG cc_start: 0.6948 (mtp-110) cc_final: 0.6373 (ppt170) REVERT: B 138 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7921 (mt-10) REVERT: B 236 MET cc_start: 0.7517 (mmt) cc_final: 0.7035 (mmp) REVERT: B 258 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.5626 (t80) REVERT: B 301 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7576 (tt) REVERT: B 327 ILE cc_start: 0.8189 (mt) cc_final: 0.7927 (mm) REVERT: C 21 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7424 (ttpt) REVERT: C 185 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7826 (tt0) REVERT: C 243 ASN cc_start: 0.7111 (t0) cc_final: 0.6623 (t0) REVERT: C 245 ASP cc_start: 0.7434 (p0) cc_final: 0.7132 (m-30) REVERT: D 17 ARG cc_start: 0.7478 (mtm-85) cc_final: 0.7240 (mtm110) REVERT: D 138 GLU cc_start: 0.7381 (tt0) cc_final: 0.7087 (tp30) REVERT: D 213 MET cc_start: 0.8506 (mmm) cc_final: 0.7998 (mtm) REVERT: D 246 TRP cc_start: 0.8802 (m100) cc_final: 0.8506 (m-90) REVERT: E 85 ARG cc_start: 0.7160 (OUTLIER) cc_final: 0.6955 (ptm160) REVERT: E 94 LYS cc_start: 0.8137 (mmtp) cc_final: 0.7912 (mmpt) REVERT: E 189 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7082 (mt-10) REVERT: E 211 GLU cc_start: 0.7051 (OUTLIER) cc_final: 0.6664 (pm20) REVERT: E 305 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8504 (mp) REVERT: J 82 GLN cc_start: 0.8280 (tt0) cc_final: 0.7762 (tp40) REVERT: L 104 GLU cc_start: 0.3993 (OUTLIER) cc_final: 0.3387 (mt-10) REVERT: K 90 ASP cc_start: 0.7508 (m-30) cc_final: 0.6848 (p0) outliers start: 66 outliers final: 51 residues processed: 344 average time/residue: 1.2762 time to fit residues: 490.8933 Evaluate side-chains 368 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 307 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 187 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 185 GLN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 49 SER Chi-restraints excluded: chain D residue 78 LYS Chi-restraints excluded: chain D residue 82 THR Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 85 ARG Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 211 GLU Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 291 SER Chi-restraints excluded: chain E residue 305 ILE Chi-restraints excluded: chain E residue 309 SER Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain I residue 91 SER Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 99 LYS Chi-restraints excluded: chain J residue 106 ASP Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 101 THR Chi-restraints excluded: chain L residue 104 GLU Chi-restraints excluded: chain K residue 31 ASP Chi-restraints excluded: chain K residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 164 optimal weight: 5.9990 chunk 68 optimal weight: 0.3980 chunk 168 optimal weight: 1.9990 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 144 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN B 189 ASN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN J 110 GLN K 5 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.142471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.113918 restraints weight = 20687.682| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.77 r_work: 0.3081 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17912 Z= 0.240 Angle : 0.584 7.789 24362 Z= 0.291 Chirality : 0.044 0.318 2807 Planarity : 0.004 0.037 2994 Dihedral : 12.265 155.280 2889 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.77 % Allowed : 22.73 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.19), residues: 2103 helix: 1.97 (0.22), residues: 567 sheet: 0.13 (0.19), residues: 664 loop : -0.40 (0.22), residues: 872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 241 HIS 0.003 0.001 HIS D 102 PHE 0.014 0.001 PHE E 236 TYR 0.023 0.002 TYR C 299 ARG 0.008 0.000 ARG B 323 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7971.18 seconds wall clock time: 141 minutes 36.46 seconds (8496.46 seconds total)