Starting phenix.real_space_refine on Sat Feb 17 04:14:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3t_22032/02_2024/6x3t_22032_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3t_22032/02_2024/6x3t_22032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3t_22032/02_2024/6x3t_22032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3t_22032/02_2024/6x3t_22032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3t_22032/02_2024/6x3t_22032_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3t_22032/02_2024/6x3t_22032_updated.pdb" } resolution = 2.55 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= 0.006 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: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 11248 2.51 5 N 2829 2.21 5 O 3241 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 73": "OE1" <-> "OE2" Residue "B PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B TYR 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 244": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 GLU 36": "OE1" <-> "OE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D ARG 187": "NH1" <-> "NH2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E ARG 176": "NH1" <-> "NH2" Residue "E ARG 185": "NH1" <-> "NH2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E ARG 197": "NH1" <-> "NH2" Residue "E ARG 207": "NH1" <-> "NH2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "E TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 327": "NH1" <-> "NH2" Residue "I TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I GLU 104": "OE1" <-> "OE2" Residue "J GLU 10": "OE1" <-> "OE2" Residue "J TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "J ARG 102": "NH1" <-> "NH2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 10": "OE1" <-> "OE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K ARG 98": "NH1" <-> "NH2" Residue "K ARG 102": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17415 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2731 Classifications: {'peptide': 334} Incomplete info: {'backbone_only': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 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: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'PFL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'PFL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 10.31, per 1000 atoms: 0.59 Number of scatterers: 17415 At special positions: 0 Unit cell: (117.99, 151.11, 130.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 97 16.00 O 3241 8.00 N 2829 7.00 C 11248 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=2.04 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.04 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.04 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.04 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=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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: 7.29 Conformation dependent library (CDL) restraints added in 2.9 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: 4018 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 26 sheets defined 29.7% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 8 through 19 Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 226 through 241 removed outlier: 4.079A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N TRP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 263 removed outlier: 3.667A pdb=" N THR A 262 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 271 removed outlier: 3.694A pdb=" N GLU A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N THR A 271 " --> pdb=" O HIS A 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 266 through 271' Processing helix chain 'A' and resid 280 through 304 Processing helix chain 'A' and resid 310 through 338 removed outlier: 3.579A pdb=" N ALA A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 12 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 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' 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 Processing helix chain 'B' and resid 231 through 246 removed outlier: 3.830A pdb=" N SER B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N PHE B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TRP B 246 " --> pdb=" O GLN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 276 Processing helix chain 'B' and resid 285 through 310 Processing helix chain 'B' and resid 315 through 346 removed outlier: 3.954A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix removed outlier: 3.685A pdb=" N ASN B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 20 Processing helix chain 'C' and resid 70 through 72 No H-bonds generated for 'chain 'C' and resid 70 through 72' Processing helix chain 'C' and resid 85 through 90 Processing helix chain 'C' and resid 219 through 224 Processing helix chain 'C' and resid 226 through 241 removed outlier: 4.094A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 269 removed outlier: 4.581A pdb=" N ASN C 265 " --> pdb=" O MET C 261 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N THR C 266 " --> pdb=" O THR C 262 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N HIS C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N LEU C 268 " --> pdb=" O ILE C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 304 Processing helix chain 'C' and resid 310 through 339 Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 11 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 88 through 93 removed outlier: 3.513A pdb=" N SER D 92 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 143 through 145 No H-bonds generated for 'chain 'D' and resid 143 through 145' 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 Processing helix chain 'D' and resid 231 through 246 removed outlier: 3.787A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TRP D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 275 removed outlier: 3.960A pdb=" N ASN D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 310 Processing helix chain 'D' and resid 315 through 344 removed outlier: 3.699A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (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 85 through 87 No H-bonds generated for 'chain 'E' and resid 85 through 87' Processing helix chain 'E' and resid 100 through 105 removed outlier: 4.892A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 256 removed outlier: 5.144A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix removed outlier: 4.004A pdb=" N SER E 254 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N PHE E 255 " --> pdb=" O SER E 251 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TRP E 256 " --> pdb=" O TRP E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 286 removed outlier: 4.154A pdb=" N SER E 286 " --> pdb=" O ILE E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 322 removed outlier: 4.552A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 355 removed outlier: 3.891A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) Proline residue: E 340 - end of helix Processing helix chain 'I' and resid 80 through 82 No H-bonds generated for 'chain 'I' and resid 80 through 82' Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing helix chain 'L' and resid 80 through 82 No H-bonds generated for 'chain 'L' and resid 80 through 82' 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: 6.507A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.574A 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: 3.698A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.453A 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: 6.831A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.954A 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: 6.110A pdb=" N THR B 39 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N GLU B 170 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL B 41 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B 126 " --> pdb=" O THR B 122 " (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: 4.442A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.565A 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: 6.470A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.750A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.796A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 167 through 171 removed outlier: 6.336A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 45 through 47 Processing sheet with id= L, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.362A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 179 through 183 removed outlier: 6.203A pdb=" N THR E 51 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N GLN E 182 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ILE E 53 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 57 through 59 Processing sheet with id= O, first strand: chain 'E' and resid 111 through 113 removed outlier: 4.543A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY E 218 " --> pdb=" O THR E 215 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 116 through 121 removed outlier: 7.060A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 4 through 7 Processing sheet with id= R, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.530A pdb=" N LYS I 102 " --> pdb=" O MET I 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'I' and resid 85 through 90 removed outlier: 6.322A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 3 through 6 Processing sheet with id= U, first strand: chain 'J' and resid 10 through 12 removed outlier: 5.957A pdb=" N LYS J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TRP J 47 " --> pdb=" O LYS J 38 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP J 57 " --> pdb=" O ASP J 52 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= W, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.210A pdb=" N LYS L 102 " --> pdb=" O MET L 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'L' and resid 84 through 90 removed outlier: 6.347A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 3 through 6 Processing sheet with id= Z, first strand: chain 'K' and resid 57 through 60 removed outlier: 3.688A pdb=" N ASP K 57 " --> pdb=" O ASP K 52 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N TYR K 33 " --> pdb=" O LYS K 99 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 766 hydrogen bonds defined for protein. 2214 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: 5.29 Time building geometry restraints manager: 7.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3864 1.33 - 1.45: 4357 1.45 - 1.58: 9461 1.58 - 1.70: 0 1.70 - 1.83: 167 Bond restraints: 17849 Sorted by residual: bond pdb=" CD ABU A 405 " pdb=" OE1 ABU A 405 " ideal model delta sigma weight residual 1.247 1.336 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" CD ABU C 405 " pdb=" OE2 ABU C 405 " ideal model delta sigma weight residual 1.250 1.336 -0.086 2.00e-02 2.50e+03 1.87e+01 bond pdb=" C1 MAN G 7 " pdb=" C2 MAN G 7 " ideal model delta sigma weight residual 1.526 1.574 -0.048 2.00e-02 2.50e+03 5.68e+00 bond pdb=" CD ABU A 405 " pdb=" OE2 ABU A 405 " ideal model delta sigma weight residual 1.250 1.206 0.044 2.00e-02 2.50e+03 4.87e+00 bond pdb=" C1 PFL D 601 " pdb=" O1 PFL D 601 " ideal model delta sigma weight residual 1.355 1.398 -0.043 2.00e-02 2.50e+03 4.58e+00 ... (remaining 17844 not shown) Histogram of bond angle deviations from ideal: 99.16 - 106.15: 415 106.15 - 113.13: 9762 113.13 - 120.12: 6244 120.12 - 127.10: 7653 127.10 - 134.09: 198 Bond angle restraints: 24272 Sorted by residual: angle pdb=" C GLY A 170 " pdb=" N ASP A 171 " pdb=" CA ASP A 171 " ideal model delta sigma weight residual 121.54 127.14 -5.60 1.91e+00 2.74e-01 8.59e+00 angle pdb=" CA TYR C 299 " pdb=" CB TYR C 299 " pdb=" CG TYR C 299 " ideal model delta sigma weight residual 113.90 108.93 4.97 1.80e+00 3.09e-01 7.61e+00 angle pdb=" C GLY C 170 " pdb=" N ASP C 171 " pdb=" CA ASP C 171 " ideal model delta sigma weight residual 121.54 126.62 -5.08 1.91e+00 2.74e-01 7.07e+00 angle pdb=" CA TYR A 299 " pdb=" CB TYR A 299 " pdb=" CG TYR A 299 " ideal model delta sigma weight residual 113.90 109.15 4.75 1.80e+00 3.09e-01 6.97e+00 angle pdb=" C3 MAN G 7 " pdb=" C2 MAN G 7 " pdb=" O2 MAN G 7 " ideal model delta sigma weight residual 111.77 104.29 7.48 3.00e+00 1.11e-01 6.21e+00 ... (remaining 24267 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 10235 21.48 - 42.96: 424 42.96 - 64.44: 84 64.44 - 85.91: 45 85.91 - 107.39: 22 Dihedral angle restraints: 10810 sinusoidal: 4556 harmonic: 6254 Sorted by residual: 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 180.00 150.67 29.33 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA VAL B 64 " pdb=" C VAL B 64 " pdb=" N PHE B 65 " pdb=" CA PHE B 65 " ideal model delta harmonic sigma weight residual 180.00 154.47 25.53 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA ILE A 47 " pdb=" C ILE A 47 " pdb=" N ASP A 48 " pdb=" CA ASP A 48 " ideal model delta harmonic sigma weight residual -180.00 -155.17 -24.83 0 5.00e+00 4.00e-02 2.47e+01 ... (remaining 10807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2189 0.053 - 0.106: 534 0.106 - 0.159: 76 0.159 - 0.212: 2 0.212 - 0.264: 5 Chirality restraints: 2806 Sorted by residual: chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN E 208 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 2803 not shown) Planarity restraints: 2991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 242 " -0.027 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO E 243 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 243 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 243 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 153 " -0.026 5.00e-02 4.00e+02 3.87e-02 2.39e+00 pdb=" N PRO B 154 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO B 154 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 154 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 299 " -0.017 2.00e-02 2.50e+03 1.05e-02 2.19e+00 pdb=" CG TYR A 299 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR A 299 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 299 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 299 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 299 " -0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 299 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 299 " -0.004 2.00e-02 2.50e+03 ... (remaining 2988 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 644 2.72 - 3.26: 16813 3.26 - 3.81: 29464 3.81 - 4.35: 37777 4.35 - 4.90: 63164 Nonbonded interactions: 147862 Sorted by model distance: nonbonded pdb=" OG1 THR B 122 " pdb=" OD1 ASP B 124 " model vdw 2.171 2.440 nonbonded pdb=" OD1 ASP B 63 " pdb=" OG1 THR B 134 " model vdw 2.184 2.440 nonbonded pdb=" OD1 ASP D 10 " pdb=" OG1 THR D 12 " model vdw 2.185 2.440 nonbonded pdb=" OG SER L 65 " pdb=" OG1 THR L 72 " model vdw 2.199 2.440 nonbonded pdb=" OD1 ASP C 101 " pdb=" OG SER C 104 " model vdw 2.219 2.440 ... (remaining 147857 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' and (resid 7 through 173 or (resid 174 and (name N or name CA or name \ C or name O )) or resid 175 through 340 or resid 404 through 405)) } ncs_group { reference = chain 'B' selection = chain 'D' } 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 4.620 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 48.730 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 : 0.005 0.089 17849 Z= 0.307 Angle : 0.662 8.142 24272 Z= 0.348 Chirality : 0.046 0.264 2806 Planarity : 0.004 0.040 2984 Dihedral : 14.711 107.393 6765 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.28 % Allowed : 7.65 % Favored : 90.07 % 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: -0.78 (0.17), residues: 2103 helix: 0.51 (0.20), residues: 582 sheet: -0.37 (0.19), residues: 652 loop : -1.26 (0.20), residues: 869 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 103 HIS 0.003 0.001 HIS E 122 PHE 0.015 0.002 PHE E 236 TYR 0.022 0.002 TYR A 299 ARG 0.006 0.001 ARG K 50 *********************** 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 368 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 325 time to evaluate : 2.852 Fit side-chains REVERT: A 14 GLU cc_start: 0.7180 (tt0) cc_final: 0.6679 (tp30) REVERT: A 318 ARG cc_start: 0.6230 (mtm110) cc_final: 0.5468 (ppt170) REVERT: A 323 PHE cc_start: 0.6019 (t80) cc_final: 0.5480 (m-80) REVERT: B 24 ASP cc_start: 0.6922 (t0) cc_final: 0.6524 (p0) REVERT: B 141 MET cc_start: 0.8444 (mtt) cc_final: 0.7962 (mtt) REVERT: B 204 GLN cc_start: 0.8199 (mm-40) cc_final: 0.7921 (tp-100) REVERT: B 271 ILE cc_start: 0.7482 (mt) cc_final: 0.7259 (mm) REVERT: B 275 ASN cc_start: 0.5850 (m-40) cc_final: 0.5607 (m-40) REVERT: B 286 MET cc_start: 0.8281 (ttp) cc_final: 0.7824 (ttp) REVERT: B 317 ARG cc_start: 0.6685 (ttt180) cc_final: 0.6373 (ttt-90) REVERT: C 90 GLN cc_start: 0.8109 (mt0) cc_final: 0.7758 (mp10) REVERT: C 182 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6971 (tp30) REVERT: C 227 MET cc_start: 0.7395 (mmt) cc_final: 0.7148 (mmt) REVERT: C 286 MET cc_start: 0.8338 (mtt) cc_final: 0.8056 (mtt) REVERT: C 303 ASN cc_start: 0.8402 (t0) cc_final: 0.8100 (t0) REVERT: C 304 TYR cc_start: 0.8049 (t80) cc_final: 0.7717 (t80) REVERT: D 24 ASP cc_start: 0.7248 (t70) cc_final: 0.6907 (p0) REVERT: D 73 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.6878 (mp0) REVERT: D 248 ASN cc_start: 0.6912 (t0) cc_final: 0.6648 (t0) REVERT: D 286 MET cc_start: 0.7738 (ttp) cc_final: 0.7535 (ttm) REVERT: D 320 LYS cc_start: 0.6816 (ttpt) cc_final: 0.6465 (ttmm) REVERT: D 324 LEU cc_start: 0.6874 (mt) cc_final: 0.6659 (mp) REVERT: E 66 ASN cc_start: 0.7678 (t0) cc_final: 0.7468 (t0) REVERT: E 168 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7487 (mt-10) REVERT: E 189 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7356 (mt-10) REVERT: E 236 PHE cc_start: 0.7911 (m-80) cc_final: 0.7645 (m-80) REVERT: I 61 ARG cc_start: 0.6766 (ptt-90) cc_final: 0.6522 (ptt90) REVERT: I 72 THR cc_start: 0.8285 (m) cc_final: 0.8062 (t) REVERT: J 19 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7015 (mttm) REVERT: J 114 VAL cc_start: 0.7418 (OUTLIER) cc_final: 0.7169 (p) REVERT: L 21 LEU cc_start: 0.7874 (mp) cc_final: 0.7653 (mt) REVERT: L 24 LYS cc_start: 0.8364 (mttt) cc_final: 0.7968 (mttp) REVERT: L 82 ASP cc_start: 0.6323 (m-30) cc_final: 0.5739 (m-30) REVERT: K 25 SER cc_start: 0.7521 (m) cc_final: 0.7045 (t) REVERT: K 61 ASP cc_start: 0.7618 (t0) cc_final: 0.7371 (t0) outliers start: 43 outliers final: 21 residues processed: 358 average time/residue: 1.4046 time to fit residues: 555.7561 Evaluate side-chains 296 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 272 time to evaluate : 2.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 162 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 187 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN B 102 HIS B 190 GLN B 229 GLN C 224 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 242 GLN ** E 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN K 6 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 17849 Z= 0.460 Angle : 0.731 9.462 24272 Z= 0.379 Chirality : 0.050 0.204 2806 Planarity : 0.006 0.080 2984 Dihedral : 10.251 81.493 2868 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 5.10 % Allowed : 11.90 % Favored : 83.01 % 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: -0.15 (0.18), residues: 2103 helix: 1.15 (0.21), residues: 583 sheet: -0.31 (0.18), residues: 684 loop : -0.68 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP K 103 HIS 0.006 0.002 HIS E 156 PHE 0.023 0.003 PHE E 236 TYR 0.036 0.003 TYR A 299 ARG 0.007 0.001 ARG E 232 *********************** 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 362 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 266 time to evaluate : 2.094 Fit side-chains REVERT: A 14 GLU cc_start: 0.7260 (tt0) cc_final: 0.6669 (tp30) REVERT: A 40 MET cc_start: 0.8559 (OUTLIER) cc_final: 0.7244 (mpt) REVERT: A 86 ARG cc_start: 0.7830 (mtm-85) cc_final: 0.7405 (mtm-85) REVERT: A 101 ASP cc_start: 0.7894 (p0) cc_final: 0.7542 (p0) REVERT: A 306 PHE cc_start: 0.5530 (t80) cc_final: 0.5222 (t80) REVERT: A 318 ARG cc_start: 0.6247 (mtm110) cc_final: 0.5461 (ppt170) REVERT: A 323 PHE cc_start: 0.5919 (t80) cc_final: 0.5489 (m-80) REVERT: B 24 ASP cc_start: 0.6912 (t0) cc_final: 0.6492 (p0) REVERT: B 93 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7648 (mmtp) REVERT: B 123 GLU cc_start: 0.8062 (OUTLIER) cc_final: 0.7833 (pt0) REVERT: B 141 MET cc_start: 0.8439 (mtt) cc_final: 0.7916 (mtt) REVERT: B 204 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7985 (tp-100) REVERT: B 271 ILE cc_start: 0.7495 (mt) cc_final: 0.7252 (mm) REVERT: B 275 ASN cc_start: 0.5975 (m-40) cc_final: 0.5720 (m-40) REVERT: B 286 MET cc_start: 0.8243 (ttp) cc_final: 0.7896 (ttp) REVERT: C 182 GLU cc_start: 0.7379 (mm-30) cc_final: 0.7014 (tp30) REVERT: C 227 MET cc_start: 0.7474 (mmt) cc_final: 0.7262 (mmt) REVERT: C 272 LEU cc_start: 0.7312 (OUTLIER) cc_final: 0.7073 (mm) REVERT: C 283 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7198 (tpt) REVERT: C 286 MET cc_start: 0.8351 (mtt) cc_final: 0.8078 (mtt) REVERT: C 303 ASN cc_start: 0.8359 (t0) cc_final: 0.8086 (t0) REVERT: C 304 TYR cc_start: 0.8024 (t80) cc_final: 0.7701 (t80) REVERT: D 24 ASP cc_start: 0.7270 (t70) cc_final: 0.6874 (p0) REVERT: D 40 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7340 (tm-30) REVERT: D 73 GLU cc_start: 0.7568 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: D 248 ASN cc_start: 0.6942 (t0) cc_final: 0.6721 (t0) REVERT: D 320 LYS cc_start: 0.6928 (ttpt) cc_final: 0.6650 (ttmm) REVERT: D 331 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7799 (tp) REVERT: E 150 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7420 (pt0) REVERT: E 168 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7639 (mt-10) REVERT: E 331 MET cc_start: 0.6857 (OUTLIER) cc_final: 0.6228 (ptp) REVERT: I 72 THR cc_start: 0.8311 (m) cc_final: 0.8042 (t) REVERT: J 114 VAL cc_start: 0.7614 (OUTLIER) cc_final: 0.7337 (p) REVERT: L 24 LYS cc_start: 0.8400 (mttt) cc_final: 0.7993 (mttp) REVERT: L 82 ASP cc_start: 0.6313 (m-30) cc_final: 0.5876 (m-30) REVERT: K 25 SER cc_start: 0.7603 (m) cc_final: 0.7113 (t) REVERT: K 61 ASP cc_start: 0.7550 (t0) cc_final: 0.7235 (t0) REVERT: K 89 GLU cc_start: 0.5797 (OUTLIER) cc_final: 0.5365 (pp20) outliers start: 96 outliers final: 55 residues processed: 330 average time/residue: 1.3234 time to fit residues: 485.7766 Evaluate side-chains 327 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 259 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 30 LYS Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 89 GLU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 203 optimal weight: 9.9990 chunk 167 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 64 optimal weight: 10.0000 chunk 151 optimal weight: 0.6980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 224 GLN B 190 GLN C 185 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17849 Z= 0.190 Angle : 0.565 7.389 24272 Z= 0.291 Chirality : 0.043 0.162 2806 Planarity : 0.004 0.053 2984 Dihedral : 8.671 77.700 2868 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.56 % Allowed : 14.45 % Favored : 82.00 % 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: 0.48 (0.18), residues: 2103 helix: 1.86 (0.22), residues: 588 sheet: 0.06 (0.19), residues: 630 loop : -0.47 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 103 HIS 0.005 0.001 HIS A 267 PHE 0.014 0.002 PHE E 338 TYR 0.034 0.002 TYR A 299 ARG 0.003 0.000 ARG K 40 *********************** 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 345 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 278 time to evaluate : 2.079 Fit side-chains REVERT: A 14 GLU cc_start: 0.7205 (tt0) cc_final: 0.6732 (tp30) REVERT: A 40 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.6969 (mpt) REVERT: A 86 ARG cc_start: 0.7715 (mtm-85) cc_final: 0.7463 (mtm-85) REVERT: A 318 ARG cc_start: 0.6315 (mtm110) cc_final: 0.5924 (mtm-85) REVERT: A 323 PHE cc_start: 0.5867 (t80) cc_final: 0.5461 (m-80) REVERT: B 21 ARG cc_start: 0.7627 (ttp-110) cc_final: 0.7222 (ttp-110) REVERT: B 24 ASP cc_start: 0.6856 (t0) cc_final: 0.6557 (p0) REVERT: B 141 MET cc_start: 0.8427 (mtt) cc_final: 0.7873 (mtt) REVERT: B 204 GLN cc_start: 0.8198 (mm-40) cc_final: 0.7964 (tp-100) REVERT: B 286 MET cc_start: 0.8207 (ttp) cc_final: 0.7817 (ttp) REVERT: B 317 ARG cc_start: 0.6816 (ttt180) cc_final: 0.6406 (ttt-90) REVERT: C 90 GLN cc_start: 0.8031 (mt0) cc_final: 0.7679 (mp-120) REVERT: C 182 GLU cc_start: 0.7330 (mm-30) cc_final: 0.7007 (tp30) REVERT: C 227 MET cc_start: 0.7523 (mmt) cc_final: 0.7321 (mmt) REVERT: C 303 ASN cc_start: 0.8328 (t0) cc_final: 0.8050 (t0) REVERT: C 304 TYR cc_start: 0.8027 (t80) cc_final: 0.7701 (t80) REVERT: D 24 ASP cc_start: 0.7249 (t70) cc_final: 0.6839 (p0) REVERT: D 73 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.6873 (mp0) REVERT: D 141 MET cc_start: 0.8329 (mtt) cc_final: 0.8038 (mtp) REVERT: D 248 ASN cc_start: 0.6979 (t0) cc_final: 0.6705 (t0) REVERT: D 320 LYS cc_start: 0.6887 (ttpt) cc_final: 0.6567 (ttmm) REVERT: D 331 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7720 (tp) REVERT: E 168 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7570 (mt-10) REVERT: E 282 ILE cc_start: 0.7787 (mm) cc_final: 0.7517 (OUTLIER) REVERT: E 331 MET cc_start: 0.6858 (OUTLIER) cc_final: 0.6285 (ptp) REVERT: I 72 THR cc_start: 0.8285 (m) cc_final: 0.8056 (t) REVERT: L 24 LYS cc_start: 0.8372 (mttt) cc_final: 0.7803 (mtmm) REVERT: L 82 ASP cc_start: 0.6224 (m-30) cc_final: 0.5714 (m-30) REVERT: K 25 SER cc_start: 0.7466 (m) cc_final: 0.7003 (t) REVERT: K 61 ASP cc_start: 0.7677 (t0) cc_final: 0.7368 (t0) REVERT: K 89 GLU cc_start: 0.5743 (pp20) cc_final: 0.5380 (pp20) outliers start: 67 outliers final: 41 residues processed: 318 average time/residue: 1.3814 time to fit residues: 486.7072 Evaluate side-chains 313 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 269 time to evaluate : 2.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 7.9990 chunk 141 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 chunk 179 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 224 GLN B 190 GLN C 185 GLN ** D 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 229 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.0908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 17849 Z= 0.352 Angle : 0.653 8.371 24272 Z= 0.338 Chirality : 0.047 0.193 2806 Planarity : 0.005 0.070 2984 Dihedral : 8.734 79.459 2855 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.99 % Allowed : 14.71 % Favored : 80.30 % 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: 0.40 (0.18), residues: 2103 helix: 1.77 (0.22), residues: 588 sheet: -0.10 (0.19), residues: 667 loop : -0.40 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 103 HIS 0.004 0.001 HIS E 156 PHE 0.020 0.002 PHE E 236 TYR 0.039 0.002 TYR A 299 ARG 0.005 0.001 ARG E 232 *********************** 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 362 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 268 time to evaluate : 2.159 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7247 (tt0) cc_final: 0.6624 (tp30) REVERT: A 21 LYS cc_start: 0.7115 (mttp) cc_final: 0.6776 (mttt) REVERT: A 40 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7074 (mpt) REVERT: A 86 ARG cc_start: 0.7794 (mtm-85) cc_final: 0.7575 (mtm-85) REVERT: A 101 ASP cc_start: 0.7868 (p0) cc_final: 0.7516 (p0) REVERT: A 283 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7229 (ttm) REVERT: A 318 ARG cc_start: 0.6247 (mtm110) cc_final: 0.5480 (ppt170) REVERT: A 323 PHE cc_start: 0.5821 (t80) cc_final: 0.5488 (m-80) REVERT: B 24 ASP cc_start: 0.6898 (t0) cc_final: 0.6566 (p0) REVERT: B 93 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7629 (mmtp) REVERT: B 123 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7763 (pt0) REVERT: B 141 MET cc_start: 0.8430 (mtt) cc_final: 0.7963 (mtt) REVERT: B 204 GLN cc_start: 0.8221 (mm-40) cc_final: 0.7975 (tp-100) REVERT: B 286 MET cc_start: 0.8221 (ttp) cc_final: 0.7948 (ttp) REVERT: B 317 ARG cc_start: 0.6853 (ttt180) cc_final: 0.6461 (ttt-90) REVERT: C 90 GLN cc_start: 0.8184 (mt0) cc_final: 0.7780 (mp-120) REVERT: C 182 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7008 (tp30) REVERT: C 272 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6905 (mm) REVERT: C 303 ASN cc_start: 0.8362 (t0) cc_final: 0.8074 (t0) REVERT: C 304 TYR cc_start: 0.8023 (t80) cc_final: 0.7686 (t80) REVERT: D 24 ASP cc_start: 0.7292 (t70) cc_final: 0.6861 (p0) REVERT: D 40 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7383 (tm-30) REVERT: D 73 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6877 (mp0) REVERT: D 248 ASN cc_start: 0.6934 (t0) cc_final: 0.6677 (t0) REVERT: D 320 LYS cc_start: 0.6900 (ttpt) cc_final: 0.6584 (ttmm) REVERT: D 331 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7787 (tp) REVERT: E 150 GLU cc_start: 0.7594 (OUTLIER) cc_final: 0.7327 (pt0) REVERT: E 168 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7600 (mt-10) REVERT: E 233 MET cc_start: 0.6436 (OUTLIER) cc_final: 0.5759 (ttm) REVERT: E 331 MET cc_start: 0.6800 (OUTLIER) cc_final: 0.6247 (ptp) REVERT: I 61 ARG cc_start: 0.6740 (ptt90) cc_final: 0.6485 (ptt90) REVERT: I 72 THR cc_start: 0.8280 (m) cc_final: 0.8024 (t) REVERT: L 18 ARG cc_start: 0.6427 (ttm-80) cc_final: 0.6013 (ttm-80) REVERT: L 24 LYS cc_start: 0.8385 (mttt) cc_final: 0.7821 (mtmm) REVERT: L 82 ASP cc_start: 0.6233 (m-30) cc_final: 0.5768 (m-30) REVERT: K 11 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6641 (tp) REVERT: K 25 SER cc_start: 0.7583 (m) cc_final: 0.7082 (t) REVERT: K 61 ASP cc_start: 0.7607 (t0) cc_final: 0.7316 (t0) outliers start: 94 outliers final: 58 residues processed: 326 average time/residue: 1.3233 time to fit residues: 479.7087 Evaluate side-chains 334 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 264 time to evaluate : 1.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 255 ILE Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 247 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 58 VAL 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 103 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 46 GLU Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 0.0010 chunk 113 optimal weight: 0.8980 chunk 2 optimal weight: 0.0060 chunk 148 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 170 optimal weight: 0.0170 chunk 138 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 179 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.3640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN C 85 ASN C 185 GLN D 87 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 17849 Z= 0.133 Angle : 0.509 6.543 24272 Z= 0.262 Chirality : 0.041 0.153 2806 Planarity : 0.004 0.046 2984 Dihedral : 7.416 70.279 2855 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.92 % Allowed : 17.05 % Favored : 80.03 % 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: 0.87 (0.19), residues: 2103 helix: 2.27 (0.22), residues: 592 sheet: 0.18 (0.19), residues: 682 loop : -0.23 (0.22), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 103 HIS 0.006 0.001 HIS A 267 PHE 0.016 0.001 PHE E 338 TYR 0.033 0.001 TYR A 299 ARG 0.003 0.000 ARG K 40 *********************** 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 347 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 292 time to evaluate : 2.050 Fit side-chains REVERT: A 14 GLU cc_start: 0.7183 (tt0) cc_final: 0.6657 (tp30) REVERT: A 40 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.6957 (mpt) REVERT: A 86 ARG cc_start: 0.7698 (mtm-85) cc_final: 0.7397 (mtm-85) REVERT: A 283 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.7111 (ttm) REVERT: A 318 ARG cc_start: 0.6246 (mtm110) cc_final: 0.5565 (ppt170) REVERT: A 323 PHE cc_start: 0.5892 (t80) cc_final: 0.5574 (m-80) REVERT: B 24 ASP cc_start: 0.6836 (t0) cc_final: 0.6607 (p0) REVERT: B 141 MET cc_start: 0.8400 (mtt) cc_final: 0.7875 (mtt) REVERT: B 286 MET cc_start: 0.8125 (ttp) cc_final: 0.7771 (ttp) REVERT: B 317 ARG cc_start: 0.6754 (ttt180) cc_final: 0.6355 (ttt-90) REVERT: C 90 GLN cc_start: 0.8048 (mt0) cc_final: 0.7706 (mp-120) REVERT: C 180 LYS cc_start: 0.7327 (mtmt) cc_final: 0.6996 (mppt) REVERT: C 182 GLU cc_start: 0.7294 (mm-30) cc_final: 0.7006 (tp30) REVERT: C 272 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6569 (mm) REVERT: C 303 ASN cc_start: 0.8260 (t0) cc_final: 0.8011 (t0) REVERT: C 304 TYR cc_start: 0.8024 (t80) cc_final: 0.7688 (t80) REVERT: D 24 ASP cc_start: 0.7294 (t70) cc_final: 0.6933 (p0) REVERT: D 73 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: D 141 MET cc_start: 0.8548 (mtp) cc_final: 0.8319 (mtt) REVERT: D 248 ASN cc_start: 0.7011 (t0) cc_final: 0.6720 (t0) REVERT: D 320 LYS cc_start: 0.6898 (ttpt) cc_final: 0.6618 (ttmm) REVERT: D 331 LEU cc_start: 0.7973 (OUTLIER) cc_final: 0.7762 (tp) REVERT: E 168 GLU cc_start: 0.7769 (mt-10) cc_final: 0.7473 (mt-10) REVERT: E 282 ILE cc_start: 0.7763 (mm) cc_final: 0.7494 (OUTLIER) REVERT: E 331 MET cc_start: 0.6776 (OUTLIER) cc_final: 0.6343 (ptp) REVERT: J 30 LYS cc_start: 0.7180 (OUTLIER) cc_final: 0.6909 (mmtp) REVERT: L 24 LYS cc_start: 0.8321 (mttt) cc_final: 0.7771 (mtmm) REVERT: L 82 ASP cc_start: 0.6277 (m-30) cc_final: 0.5811 (m-30) REVERT: K 61 ASP cc_start: 0.7605 (t0) cc_final: 0.7358 (t0) outliers start: 55 outliers final: 30 residues processed: 326 average time/residue: 1.3229 time to fit residues: 480.4416 Evaluate side-chains 310 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 274 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 82 GLN Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 0.0970 chunk 180 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 166 optimal weight: 0.0010 chunk 92 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN B 190 GLN C 85 ASN C 185 GLN D 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17849 Z= 0.139 Angle : 0.504 6.794 24272 Z= 0.258 Chirality : 0.041 0.170 2806 Planarity : 0.004 0.043 2984 Dihedral : 6.658 62.070 2838 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.03 % Allowed : 17.58 % Favored : 79.39 % 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: 1.07 (0.19), residues: 2103 helix: 2.45 (0.22), residues: 590 sheet: 0.22 (0.19), residues: 698 loop : -0.04 (0.23), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 103 HIS 0.005 0.001 HIS A 267 PHE 0.034 0.001 PHE A 306 TYR 0.031 0.001 TYR A 299 ARG 0.004 0.000 ARG K 40 *********************** 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 332 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 275 time to evaluate : 2.073 Fit side-chains REVERT: A 14 GLU cc_start: 0.7213 (tt0) cc_final: 0.6682 (tp30) REVERT: A 40 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.6957 (mpt) REVERT: A 49 MET cc_start: 0.6218 (OUTLIER) cc_final: 0.5589 (ptt) REVERT: A 86 ARG cc_start: 0.7730 (mtm-85) cc_final: 0.7426 (mtm-85) REVERT: A 306 PHE cc_start: 0.5219 (t80) cc_final: 0.5014 (t80) REVERT: A 318 ARG cc_start: 0.6331 (mtm110) cc_final: 0.5601 (ppt170) REVERT: A 323 PHE cc_start: 0.5811 (t80) cc_final: 0.5504 (m-80) REVERT: B 24 ASP cc_start: 0.6885 (t0) cc_final: 0.6666 (p0) REVERT: B 93 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7634 (mmtp) REVERT: B 141 MET cc_start: 0.8390 (mtt) cc_final: 0.7910 (mtt) REVERT: B 286 MET cc_start: 0.8136 (ttp) cc_final: 0.7798 (ttp) REVERT: B 317 ARG cc_start: 0.6793 (ttt180) cc_final: 0.6376 (ttt-90) REVERT: C 90 GLN cc_start: 0.8055 (mt0) cc_final: 0.7639 (mp10) REVERT: C 180 LYS cc_start: 0.7294 (mtmt) cc_final: 0.6880 (mppt) REVERT: C 182 GLU cc_start: 0.7285 (mm-30) cc_final: 0.7011 (tp30) REVERT: C 272 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6520 (mm) REVERT: C 303 ASN cc_start: 0.8283 (t0) cc_final: 0.8021 (t0) REVERT: D 73 GLU cc_start: 0.7423 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: D 141 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8302 (mtt) REVERT: D 248 ASN cc_start: 0.7029 (t0) cc_final: 0.6718 (t0) REVERT: D 320 LYS cc_start: 0.6892 (ttpt) cc_final: 0.6598 (ttmm) REVERT: D 331 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7674 (tp) REVERT: E 168 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7474 (mt-10) REVERT: E 282 ILE cc_start: 0.7697 (mm) cc_final: 0.7478 (OUTLIER) REVERT: E 331 MET cc_start: 0.6764 (OUTLIER) cc_final: 0.6333 (ptp) REVERT: J 30 LYS cc_start: 0.7152 (OUTLIER) cc_final: 0.6878 (mmtp) REVERT: L 24 LYS cc_start: 0.8297 (mttt) cc_final: 0.7753 (mtmm) REVERT: L 82 ASP cc_start: 0.6297 (m-30) cc_final: 0.5814 (m-30) REVERT: K 61 ASP cc_start: 0.7590 (t0) cc_final: 0.7290 (t0) outliers start: 57 outliers final: 30 residues processed: 310 average time/residue: 1.3318 time to fit residues: 458.6577 Evaluate side-chains 306 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 268 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 141 MET Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 6.9990 chunk 22 optimal weight: 0.4980 chunk 114 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 121 optimal weight: 1.9990 chunk 92 optimal weight: 6.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN C 85 ASN C 185 GLN D 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17849 Z= 0.261 Angle : 0.587 7.633 24272 Z= 0.302 Chirality : 0.045 0.190 2806 Planarity : 0.004 0.042 2984 Dihedral : 7.133 65.476 2835 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.82 % Allowed : 17.15 % Favored : 79.02 % 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: 0.95 (0.19), residues: 2103 helix: 2.25 (0.22), residues: 588 sheet: 0.21 (0.19), residues: 664 loop : -0.09 (0.22), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 103 HIS 0.005 0.001 HIS A 267 PHE 0.016 0.002 PHE E 169 TYR 0.039 0.002 TYR A 299 ARG 0.004 0.000 ARG E 232 *********************** 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 345 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 273 time to evaluate : 2.048 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7232 (tt0) cc_final: 0.6691 (tp30) REVERT: A 40 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7074 (mpt) REVERT: A 86 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7436 (mtm-85) REVERT: A 101 ASP cc_start: 0.7780 (p0) cc_final: 0.7449 (p0) REVERT: A 318 ARG cc_start: 0.6357 (mtm110) cc_final: 0.5576 (ppt170) REVERT: A 323 PHE cc_start: 0.5855 (t80) cc_final: 0.5504 (m-80) REVERT: B 24 ASP cc_start: 0.6885 (t0) cc_final: 0.6645 (p0) REVERT: B 93 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7624 (mmtp) REVERT: B 141 MET cc_start: 0.8423 (mtt) cc_final: 0.7967 (mtt) REVERT: B 286 MET cc_start: 0.8202 (ttp) cc_final: 0.7893 (ttp) REVERT: B 317 ARG cc_start: 0.6826 (ttt180) cc_final: 0.6515 (ttt-90) REVERT: C 90 GLN cc_start: 0.8126 (mt0) cc_final: 0.7660 (mp10) REVERT: C 182 GLU cc_start: 0.7322 (mm-30) cc_final: 0.7028 (tp30) REVERT: C 272 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6710 (mm) REVERT: C 303 ASN cc_start: 0.8312 (t0) cc_final: 0.8026 (t0) REVERT: C 304 TYR cc_start: 0.8031 (t80) cc_final: 0.7698 (t80) REVERT: D 24 ASP cc_start: 0.7264 (t70) cc_final: 0.6863 (p0) REVERT: D 40 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7401 (tm-30) REVERT: D 73 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.6926 (mp0) REVERT: D 248 ASN cc_start: 0.6979 (t0) cc_final: 0.6686 (t0) REVERT: D 320 LYS cc_start: 0.6800 (ttpt) cc_final: 0.6488 (ttmm) REVERT: D 331 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7659 (tp) REVERT: E 168 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7443 (mt-10) REVERT: E 233 MET cc_start: 0.6322 (OUTLIER) cc_final: 0.5802 (ttm) REVERT: E 331 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.6236 (ptp) REVERT: L 13 MET cc_start: 0.4918 (mmm) cc_final: 0.4688 (mmp) REVERT: L 24 LYS cc_start: 0.8315 (mttt) cc_final: 0.7777 (mtmm) REVERT: L 82 ASP cc_start: 0.6457 (m-30) cc_final: 0.5964 (m-30) REVERT: K 11 LEU cc_start: 0.6978 (OUTLIER) cc_final: 0.6677 (tp) REVERT: K 25 SER cc_start: 0.7607 (m) cc_final: 0.7357 (p) REVERT: K 61 ASP cc_start: 0.7597 (t0) cc_final: 0.7305 (t0) REVERT: K 89 GLU cc_start: 0.5751 (pp20) cc_final: 0.5346 (pp20) outliers start: 72 outliers final: 46 residues processed: 323 average time/residue: 1.3088 time to fit residues: 473.2520 Evaluate side-chains 325 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 270 time to evaluate : 1.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.0870 chunk 79 optimal weight: 0.6980 chunk 119 optimal weight: 0.9980 chunk 60 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 overall best weight: 1.7562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN C 85 ASN C 185 GLN L 42 GLN K 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17849 Z= 0.244 Angle : 0.583 11.258 24272 Z= 0.299 Chirality : 0.044 0.185 2806 Planarity : 0.004 0.044 2984 Dihedral : 7.216 67.091 2835 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.20 % Allowed : 16.94 % Favored : 78.86 % 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: 0.92 (0.19), residues: 2103 helix: 2.24 (0.22), residues: 586 sheet: 0.17 (0.19), residues: 665 loop : -0.09 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 103 HIS 0.005 0.001 HIS A 267 PHE 0.025 0.002 PHE A 306 TYR 0.039 0.002 TYR A 299 ARG 0.005 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 353 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 274 time to evaluate : 2.066 Fit side-chains revert: symmetry clash REVERT: A 14 GLU cc_start: 0.7201 (tt0) cc_final: 0.6649 (tp30) REVERT: A 21 LYS cc_start: 0.7226 (mttp) cc_final: 0.6651 (mttp) REVERT: A 40 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7061 (mpt) REVERT: A 86 ARG cc_start: 0.7701 (mtm-85) cc_final: 0.7413 (mtm-85) REVERT: A 101 ASP cc_start: 0.7772 (p0) cc_final: 0.7432 (p0) REVERT: A 318 ARG cc_start: 0.6277 (mtm110) cc_final: 0.5514 (ppt170) REVERT: A 323 PHE cc_start: 0.5924 (t80) cc_final: 0.5579 (m-80) REVERT: B 24 ASP cc_start: 0.6871 (t0) cc_final: 0.6643 (p0) REVERT: B 93 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7626 (mmtp) REVERT: B 141 MET cc_start: 0.8427 (mtt) cc_final: 0.7973 (mtt) REVERT: B 286 MET cc_start: 0.8186 (ttp) cc_final: 0.7878 (ttp) REVERT: B 317 ARG cc_start: 0.6814 (ttt180) cc_final: 0.6497 (ttt-90) REVERT: C 90 GLN cc_start: 0.8183 (mt0) cc_final: 0.7728 (mp10) REVERT: C 180 LYS cc_start: 0.7424 (mtmt) cc_final: 0.7086 (mppt) REVERT: C 182 GLU cc_start: 0.7326 (mm-30) cc_final: 0.7040 (tp30) REVERT: C 303 ASN cc_start: 0.8306 (t0) cc_final: 0.8022 (t0) REVERT: C 304 TYR cc_start: 0.8019 (t80) cc_final: 0.7685 (t80) REVERT: D 24 ASP cc_start: 0.7262 (t70) cc_final: 0.6883 (p0) REVERT: D 40 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7416 (tm-30) REVERT: D 73 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.6918 (mp0) REVERT: D 248 ASN cc_start: 0.7023 (t0) cc_final: 0.6717 (t0) REVERT: D 320 LYS cc_start: 0.6802 (ttpt) cc_final: 0.6488 (ttmm) REVERT: D 331 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7608 (tp) REVERT: E 150 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7317 (pt0) REVERT: E 168 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7504 (mt-10) REVERT: E 233 MET cc_start: 0.6313 (OUTLIER) cc_final: 0.5774 (ttm) REVERT: E 282 ILE cc_start: 0.7610 (mm) cc_final: 0.7392 (mm) REVERT: E 331 MET cc_start: 0.6827 (OUTLIER) cc_final: 0.6224 (ptp) REVERT: J 30 LYS cc_start: 0.7186 (OUTLIER) cc_final: 0.6887 (mmtp) REVERT: L 13 MET cc_start: 0.4934 (mmm) cc_final: 0.4693 (mmp) REVERT: L 24 LYS cc_start: 0.8323 (mttt) cc_final: 0.7770 (mtmm) REVERT: L 82 ASP cc_start: 0.6444 (m-30) cc_final: 0.5935 (m-30) REVERT: K 11 LEU cc_start: 0.6976 (OUTLIER) cc_final: 0.6680 (tp) REVERT: K 25 SER cc_start: 0.7539 (m) cc_final: 0.7293 (p) REVERT: K 61 ASP cc_start: 0.7583 (t0) cc_final: 0.7279 (t0) REVERT: K 89 GLU cc_start: 0.5732 (pp20) cc_final: 0.5352 (pp20) outliers start: 79 outliers final: 53 residues processed: 325 average time/residue: 1.2922 time to fit residues: 467.9588 Evaluate side-chains 336 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 273 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 40 GLU Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 233 MET Chi-restraints excluded: chain E residue 268 LEU Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 15 VAL Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 19 LYS Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 0.4980 chunk 191 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 145 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 168 optimal weight: 0.7980 chunk 175 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 190 GLN C 85 ASN C 185 GLN L 42 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17849 Z= 0.196 Angle : 0.559 10.654 24272 Z= 0.285 Chirality : 0.043 0.176 2806 Planarity : 0.004 0.043 2984 Dihedral : 7.025 65.439 2835 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.45 % Allowed : 17.68 % Favored : 78.86 % 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: 1.03 (0.19), residues: 2103 helix: 2.31 (0.22), residues: 588 sheet: 0.19 (0.19), residues: 663 loop : 0.04 (0.22), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 103 HIS 0.005 0.001 HIS A 267 PHE 0.028 0.002 PHE A 306 TYR 0.038 0.002 TYR A 299 ARG 0.005 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 339 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 274 time to evaluate : 2.043 Fit side-chains REVERT: A 14 GLU cc_start: 0.7216 (tt0) cc_final: 0.6676 (tp30) REVERT: A 21 LYS cc_start: 0.7240 (mttp) cc_final: 0.6722 (mttp) REVERT: A 40 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.6981 (mpt) REVERT: A 49 MET cc_start: 0.6343 (OUTLIER) cc_final: 0.5875 (ptt) REVERT: A 86 ARG cc_start: 0.7714 (mtm-85) cc_final: 0.7412 (mtm-85) REVERT: A 318 ARG cc_start: 0.6276 (mtm110) cc_final: 0.5562 (ppt170) REVERT: A 323 PHE cc_start: 0.5818 (t80) cc_final: 0.5579 (m-80) REVERT: B 24 ASP cc_start: 0.6894 (t0) cc_final: 0.6664 (p0) REVERT: B 93 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7628 (mmtp) REVERT: B 141 MET cc_start: 0.8408 (mtt) cc_final: 0.7917 (mtt) REVERT: B 286 MET cc_start: 0.8176 (ttp) cc_final: 0.7860 (ttp) REVERT: B 317 ARG cc_start: 0.6839 (ttt180) cc_final: 0.6467 (ttt-90) REVERT: C 9 MET cc_start: 0.6749 (OUTLIER) cc_final: 0.6512 (mtt) REVERT: C 90 GLN cc_start: 0.8094 (mt0) cc_final: 0.7654 (mp10) REVERT: C 180 LYS cc_start: 0.7562 (mtmt) cc_final: 0.7203 (mppt) REVERT: C 182 GLU cc_start: 0.7317 (mm-30) cc_final: 0.7035 (tp30) REVERT: C 303 ASN cc_start: 0.8284 (t0) cc_final: 0.8009 (t0) REVERT: C 304 TYR cc_start: 0.8044 (t80) cc_final: 0.7727 (t80) REVERT: C 309 GLN cc_start: 0.5756 (OUTLIER) cc_final: 0.5556 (pt0) REVERT: D 24 ASP cc_start: 0.7300 (t70) cc_final: 0.6938 (p0) REVERT: D 73 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6936 (mp0) REVERT: D 248 ASN cc_start: 0.7023 (t0) cc_final: 0.6712 (t0) REVERT: D 320 LYS cc_start: 0.6794 (ttpt) cc_final: 0.6522 (ttmm) REVERT: D 331 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7598 (tp) REVERT: E 168 GLU cc_start: 0.7738 (mt-10) cc_final: 0.7447 (mt-10) REVERT: E 282 ILE cc_start: 0.7619 (mm) cc_final: 0.7412 (mm) REVERT: E 331 MET cc_start: 0.6819 (OUTLIER) cc_final: 0.6269 (ptp) REVERT: J 30 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6901 (mmtp) REVERT: L 13 MET cc_start: 0.4863 (mmm) cc_final: 0.4407 (mmp) REVERT: L 24 LYS cc_start: 0.8310 (mttt) cc_final: 0.7770 (mtmm) REVERT: L 82 ASP cc_start: 0.6444 (m-30) cc_final: 0.5954 (m-30) REVERT: K 11 LEU cc_start: 0.6972 (OUTLIER) cc_final: 0.6676 (tp) REVERT: K 25 SER cc_start: 0.7549 (m) cc_final: 0.7296 (p) REVERT: K 61 ASP cc_start: 0.7583 (t0) cc_final: 0.7292 (t0) outliers start: 65 outliers final: 44 residues processed: 313 average time/residue: 1.3050 time to fit residues: 454.9798 Evaluate side-chains 327 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 273 time to evaluate : 2.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 9 MET Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 309 GLN Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain J residue 71 THR Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 206 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 100 optimal weight: 0.0570 chunk 130 optimal weight: 9.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN C 85 ASN C 185 GLN D 151 HIS ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17849 Z= 0.192 Angle : 0.561 10.558 24272 Z= 0.286 Chirality : 0.043 0.176 2806 Planarity : 0.004 0.038 2984 Dihedral : 6.932 63.661 2835 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.35 % Allowed : 18.11 % Favored : 78.54 % 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: 1.02 (0.19), residues: 2103 helix: 2.30 (0.22), residues: 590 sheet: 0.19 (0.19), residues: 663 loop : 0.04 (0.22), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 103 HIS 0.005 0.001 HIS A 267 PHE 0.052 0.002 PHE A 306 TYR 0.037 0.002 TYR A 299 ARG 0.006 0.000 ARG K 40 ********************** 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 342 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 279 time to evaluate : 1.946 Fit side-chains REVERT: A 14 GLU cc_start: 0.7225 (tt0) cc_final: 0.6676 (tp30) REVERT: A 21 LYS cc_start: 0.7250 (mttp) cc_final: 0.6688 (mttp) REVERT: A 40 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.6983 (mpt) REVERT: A 49 MET cc_start: 0.6339 (OUTLIER) cc_final: 0.5873 (ptt) REVERT: A 86 ARG cc_start: 0.7712 (mtm-85) cc_final: 0.7406 (mtm-85) REVERT: A 101 ASP cc_start: 0.7731 (p0) cc_final: 0.7372 (p0) REVERT: A 318 ARG cc_start: 0.6272 (mtm110) cc_final: 0.5562 (ppt170) REVERT: A 323 PHE cc_start: 0.5823 (t80) cc_final: 0.5577 (m-80) REVERT: B 24 ASP cc_start: 0.6906 (t0) cc_final: 0.6688 (p0) REVERT: B 93 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7631 (mmtp) REVERT: B 141 MET cc_start: 0.8408 (mtt) cc_final: 0.7918 (mtt) REVERT: B 286 MET cc_start: 0.8175 (ttp) cc_final: 0.7861 (ttp) REVERT: B 317 ARG cc_start: 0.6833 (ttt180) cc_final: 0.6465 (ttt-90) REVERT: C 90 GLN cc_start: 0.8096 (mt0) cc_final: 0.7655 (mp10) REVERT: C 180 LYS cc_start: 0.7573 (mtmt) cc_final: 0.7260 (mppt) REVERT: C 182 GLU cc_start: 0.7274 (mm-30) cc_final: 0.7030 (tp30) REVERT: C 303 ASN cc_start: 0.8276 (t0) cc_final: 0.8002 (t0) REVERT: D 24 ASP cc_start: 0.7305 (t70) cc_final: 0.6947 (p0) REVERT: D 73 GLU cc_start: 0.7559 (OUTLIER) cc_final: 0.6975 (mp0) REVERT: D 248 ASN cc_start: 0.7020 (t0) cc_final: 0.6705 (t0) REVERT: D 320 LYS cc_start: 0.6790 (ttpt) cc_final: 0.6518 (ttmm) REVERT: D 331 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7588 (tp) REVERT: E 168 GLU cc_start: 0.7737 (mt-10) cc_final: 0.7445 (mt-10) REVERT: E 313 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7366 (tm-30) REVERT: E 331 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.6256 (ptp) REVERT: J 30 LYS cc_start: 0.7178 (OUTLIER) cc_final: 0.6872 (mmtp) REVERT: L 13 MET cc_start: 0.4687 (mmm) cc_final: 0.4429 (mmp) REVERT: L 24 LYS cc_start: 0.8337 (mttt) cc_final: 0.7775 (mtmm) REVERT: L 82 ASP cc_start: 0.6444 (m-30) cc_final: 0.5946 (m-30) REVERT: K 25 SER cc_start: 0.7520 (m) cc_final: 0.7273 (p) REVERT: K 61 ASP cc_start: 0.7583 (t0) cc_final: 0.7294 (t0) REVERT: K 89 GLU cc_start: 0.5732 (pp20) cc_final: 0.5366 (pp20) outliers start: 63 outliers final: 43 residues processed: 315 average time/residue: 1.3505 time to fit residues: 474.7426 Evaluate side-chains 322 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 272 time to evaluate : 2.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 40 MET Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 53 VAL Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 331 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 251 VAL Chi-restraints excluded: chain C residue 283 MET Chi-restraints excluded: chain D residue 73 GLU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 130 THR Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 331 LEU Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 55 THR Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 216 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain E residue 285 LYS Chi-restraints excluded: chain E residue 298 LEU Chi-restraints excluded: chain E residue 312 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 337 ILE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 22 SER Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 11 LEU Chi-restraints excluded: chain J residue 30 LYS Chi-restraints excluded: chain J residue 90 ASP Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 116 VAL Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 41 GLU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 83 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 151 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 68 optimal weight: 0.0370 chunk 168 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 144 optimal weight: 0.7980 overall best weight: 1.3662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 190 GLN C 85 ASN C 185 GLN ** L 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.133868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.108405 restraints weight = 21659.398| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.10 r_work: 0.3037 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17849 Z= 0.207 Angle : 0.572 10.411 24272 Z= 0.291 Chirality : 0.043 0.179 2806 Planarity : 0.004 0.037 2984 Dihedral : 6.933 63.040 2835 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.08 % Allowed : 18.43 % Favored : 78.49 % 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: 0.97 (0.19), residues: 2103 helix: 2.26 (0.22), residues: 592 sheet: 0.14 (0.19), residues: 675 loop : 0.01 (0.22), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 103 HIS 0.005 0.001 HIS A 267 PHE 0.036 0.002 PHE A 306 TYR 0.037 0.002 TYR A 299 ARG 0.006 0.000 ARG K 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7446.46 seconds wall clock time: 132 minutes 48.06 seconds (7968.06 seconds total)