Starting phenix.real_space_refine on Sat Feb 17 04:33:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd2_27332/02_2024/8dd2_27332_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd2_27332/02_2024/8dd2_27332.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd2_27332/02_2024/8dd2_27332_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd2_27332/02_2024/8dd2_27332_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd2_27332/02_2024/8dd2_27332_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd2_27332/02_2024/8dd2_27332.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd2_27332/02_2024/8dd2_27332.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd2_27332/02_2024/8dd2_27332_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd2_27332/02_2024/8dd2_27332_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 11282 2.51 5 N 2838 2.21 5 O 3242 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A ARG 169": "NH1" <-> "NH2" Residue "A ARG 207": "NH1" <-> "NH2" 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 GLU 59": "OE1" <-> "OE2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C GLU 147": "OE1" <-> "OE2" Residue "C TYR 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 318": "NH1" <-> "NH2" Residue "D ARG 17": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D ARG 173": "NH1" <-> "NH2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E ARG 176": "NH1" <-> "NH2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E ARG 197": "NH1" <-> "NH2" Residue "E GLU 313": "OE1" <-> "OE2" Residue "E ARG 327": "NH1" <-> "NH2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "J ARG 102": "NH1" <-> "NH2" Residue "L GLU 27": "OE1" <-> "OE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 10": "OE1" <-> "OE2" Residue "K GLU 89": "OE1" <-> "OE2" Residue "K ARG 98": "NH1" <-> "NH2" Residue "K ARG 102": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17459 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2729 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {'ABU': 1, 'NAG': 1, 'R5R': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {'ABU': 1, 'NAG': 1, 'R5R': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'R5R': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.50, per 1000 atoms: 0.54 Number of scatterers: 17459 At special positions: 0 Unit cell: (130.938, 139.278, 120.93, 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 3242 8.00 N 2838 7.00 C 11282 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, 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 401 " - " ASN A 80 " " NAG C 401 " - " 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 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.38 Conformation dependent library (CDL) restraints added in 3.3 seconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 28 sheets defined 30.5% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.37 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 218 through 241 removed outlier: 3.737A pdb=" N LEU A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N MET A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix removed outlier: 4.048A pdb=" N TRP A 237 " --> pdb=" O THR A 233 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL A 238 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N TRP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 271 removed outlier: 3.526A pdb=" N GLU A 270 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR A 271 " --> pdb=" O HIS A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 308 removed outlier: 4.616A pdb=" N PHE A 307 " --> pdb=" O ASN A 303 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N SER A 308 " --> pdb=" O TYR A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 339 removed outlier: 4.364A pdb=" N ASP A 317 " --> pdb=" O ALA A 313 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 318 " --> pdb=" O ALA A 314 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 88 through 93 Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 224 through 246 removed outlier: 5.198A pdb=" N LEU B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix removed outlier: 4.172A pdb=" N SER B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N TRP B 246 " --> pdb=" O GLN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 276 removed outlier: 3.506A pdb=" N ARG B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 309 Processing helix chain 'B' and resid 315 through 346 removed outlier: 3.828A pdb=" N ARG B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Proline residue: B 330 - end of helix removed outlier: 3.690A pdb=" N ASN B 346 " --> pdb=" O ALA B 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 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 89 Processing helix chain 'C' and resid 140 through 142 No H-bonds generated for 'chain 'C' and resid 140 through 142' Processing helix chain 'C' and resid 218 through 241 removed outlier: 3.728A pdb=" N LEU C 223 " --> pdb=" O GLY C 219 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N MET C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix removed outlier: 3.577A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 271 removed outlier: 3.741A pdb=" N THR C 271 " --> pdb=" O HIS C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 304 Processing helix chain 'C' and resid 310 through 338 removed outlier: 3.565A pdb=" N ILE C 322 " --> pdb=" O ARG C 318 " (cutoff:3.500A) Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 13 through 23 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 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 244 removed outlier: 4.187A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 276 removed outlier: 3.576A pdb=" N ASN D 275 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER D 276 " --> pdb=" O SER D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 310 Processing helix chain 'D' and resid 315 through 345 removed outlier: 3.810A 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 35 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 102 No H-bonds generated for 'chain 'E' and resid 100 through 102' Processing helix chain 'E' and resid 234 through 254 removed outlier: 4.776A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix removed outlier: 3.848A pdb=" N SER E 254 " --> pdb=" O LEU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 286 removed outlier: 3.522A pdb=" N SER E 286 " --> pdb=" O ILE E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 323 removed outlier: 4.162A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 356 Proline residue: E 340 - end of helix Processing helix chain 'J' and resid 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' 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 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 164 through 168 removed outlier: 6.353A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.333A 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: 3.636A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.622A 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: 6.875A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.798A 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: 6.429A pdb=" N THR B 39 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N GLU B 170 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL B 41 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 45 through 47 Processing sheet with id= F, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.283A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N LEU B 193 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 104 through 109 removed outlier: 6.963A pdb=" N ARG B 136 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N SER B 107 " --> pdb=" O THR B 134 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR B 134 " --> pdb=" O SER B 107 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.416A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.943A pdb=" N MET C 49 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.857A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.819A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 167 through 171 removed outlier: 6.390A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 45 through 47 Processing sheet with id= N, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.142A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 179 through 182 removed outlier: 6.080A pdb=" N THR E 51 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N GLN E 182 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ILE E 53 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 6.604A 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: 6.501A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N ILE E 62 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N THR E 73 " --> pdb=" O ILE E 62 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 57 through 59 Processing sheet with id= Q, first strand: chain 'E' and resid 111 through 113 removed outlier: 4.707A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 116 through 121 removed outlier: 6.881A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'I' and resid 4 through 7 Processing sheet with id= T, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.281A pdb=" N LYS I 102 " --> pdb=" O MET I 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'I' and resid 85 through 90 removed outlier: 6.429A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 3 through 6 removed outlier: 3.725A pdb=" N THR J 78 " --> pdb=" O ASP J 73 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.841A pdb=" N THR J 115 " --> pdb=" O GLU J 10 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N LYS J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N TRP J 47 " --> pdb=" O LYS J 38 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ASP J 57 " --> pdb=" O ASP J 52 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= Y, first strand: chain 'L' and resid 85 through 90 removed outlier: 5.943A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.532A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL K 18 " --> pdb=" O LEU K 83 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'K' and resid 10 through 12 removed outlier: 3.651A pdb=" N GLY K 49 " --> pdb=" O TRP K 36 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N LYS K 38 " --> pdb=" O TRP K 47 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N TRP K 47 " --> pdb=" O LYS K 38 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP K 57 " --> pdb=" O ASP K 52 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'K' and resid 97 through 99 removed outlier: 4.083A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 777 hydrogen bonds defined for protein. 2238 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: 5.25 Time building geometry restraints manager: 7.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5338 1.34 - 1.46: 4362 1.46 - 1.58: 8032 1.58 - 1.70: 0 1.70 - 1.82: 167 Bond restraints: 17899 Sorted by residual: bond pdb=" C19 R5R D 601 " pdb=" N21 R5R D 601 " ideal model delta sigma weight residual 1.452 1.335 0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" C19 R5R A 402 " pdb=" N21 R5R A 402 " ideal model delta sigma weight residual 1.452 1.342 0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" C19 R5R C 402 " pdb=" N21 R5R C 402 " ideal model delta sigma weight residual 1.452 1.344 0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C MET D 114 " pdb=" N PRO D 115 " ideal model delta sigma weight residual 1.330 1.358 -0.028 1.19e-02 7.06e+03 5.52e+00 bond pdb=" C08 R5R A 402 " pdb=" N16 R5R A 402 " ideal model delta sigma weight residual 1.325 1.369 -0.044 2.00e-02 2.50e+03 4.83e+00 ... (remaining 17894 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.76: 339 105.76 - 112.83: 9740 112.83 - 119.90: 5711 119.90 - 126.96: 8318 126.96 - 134.03: 238 Bond angle restraints: 24346 Sorted by residual: angle pdb=" C05 R5R A 402 " pdb=" C08 R5R A 402 " pdb=" N16 R5R A 402 " ideal model delta sigma weight residual 92.59 125.51 -32.92 3.00e+00 1.11e-01 1.20e+02 angle pdb=" C05 R5R D 601 " pdb=" C08 R5R D 601 " pdb=" N16 R5R D 601 " ideal model delta sigma weight residual 92.59 125.36 -32.77 3.00e+00 1.11e-01 1.19e+02 angle pdb=" C05 R5R C 402 " pdb=" C08 R5R C 402 " pdb=" N16 R5R C 402 " ideal model delta sigma weight residual 92.59 124.14 -31.55 3.00e+00 1.11e-01 1.11e+02 angle pdb=" C05 R5R A 402 " pdb=" C08 R5R A 402 " pdb=" C09 R5R A 402 " ideal model delta sigma weight residual 149.89 127.09 22.80 3.00e+00 1.11e-01 5.78e+01 angle pdb=" C05 R5R D 601 " pdb=" C08 R5R D 601 " pdb=" C09 R5R D 601 " ideal model delta sigma weight residual 149.89 127.31 22.58 3.00e+00 1.11e-01 5.66e+01 ... (remaining 24341 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.48: 10133 21.48 - 42.96: 550 42.96 - 64.45: 71 64.45 - 85.93: 44 85.93 - 107.41: 16 Dihedral angle restraints: 10814 sinusoidal: 4558 harmonic: 6256 Sorted by residual: dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 165 " pdb=" CB CYS E 165 " ideal model delta sinusoidal sigma weight residual -86.00 -34.99 -51.01 1 1.00e+01 1.00e-02 3.56e+01 dihedral pdb=" CA CYS E 165 " pdb=" C CYS E 165 " pdb=" N PRO E 166 " pdb=" CA PRO E 166 " ideal model delta harmonic sigma weight residual 180.00 -156.16 -23.84 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CB CYS C 136 " pdb=" SG CYS C 136 " pdb=" SG CYS C 150 " pdb=" CB CYS C 150 " ideal model delta sinusoidal sigma weight residual 93.00 54.81 38.19 1 1.00e+01 1.00e-02 2.06e+01 ... (remaining 10811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 2795 0.163 - 0.326: 7 0.326 - 0.489: 2 0.489 - 0.652: 2 0.652 - 0.815: 1 Chirality restraints: 2807 Sorted by residual: chirality pdb=" C1 MAN G 9 " pdb=" O2 MAN G 8 " pdb=" C2 MAN G 9 " pdb=" O5 MAN G 9 " both_signs ideal model delta sigma weight residual False 2.40 2.16 0.24 2.00e-02 2.50e+03 1.49e+02 chirality pdb=" C1 MAN G 7 " pdb=" O6 BMA G 3 " pdb=" C2 MAN G 7 " pdb=" O5 MAN G 7 " both_signs ideal model delta sigma weight residual False 2.40 2.21 0.19 2.00e-02 2.50e+03 9.00e+01 chirality pdb=" C1 MAN G 10 " pdb=" O3 MAN G 7 " pdb=" C2 MAN G 10 " pdb=" O5 MAN G 10 " both_signs ideal model delta sigma weight residual False 2.40 2.28 0.12 2.00e-02 2.50e+03 3.60e+01 ... (remaining 2804 not shown) Planarity restraints: 2998 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " -0.336 2.00e-02 2.50e+03 2.88e-01 1.04e+03 pdb=" C7 NAG M 1 " 0.083 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " -0.166 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " 0.509 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.211 2.00e-02 2.50e+03 1.74e-01 3.80e+02 pdb=" C7 NAG M 2 " 0.057 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.152 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.284 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 80 " 0.031 2.00e-02 2.50e+03 3.46e-02 1.50e+01 pdb=" CG ASN A 80 " -0.013 2.00e-02 2.50e+03 pdb=" OD1 ASN A 80 " -0.001 2.00e-02 2.50e+03 pdb=" ND2 ASN A 80 " -0.057 2.00e-02 2.50e+03 pdb=" C1 NAG A 401 " 0.040 2.00e-02 2.50e+03 ... (remaining 2995 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 239 2.61 - 3.18: 15695 3.18 - 3.76: 26977 3.76 - 4.33: 40238 4.33 - 4.90: 66149 Nonbonded interactions: 149298 Sorted by model distance: nonbonded pdb=" O LEU A 259 " pdb=" OG1 THR A 262 " model vdw 2.041 2.440 nonbonded pdb=" OG1 THR A 202 " pdb=" OE2 ABU A 403 " model vdw 2.119 2.440 nonbonded pdb=" O PHE B 296 " pdb=" OG SER B 299 " model vdw 2.123 2.440 nonbonded pdb=" OH TYR A 97 " pdb=" OE2 GLU A 155 " model vdw 2.131 2.440 nonbonded pdb=" OG SER C 211 " pdb=" O7 NAG H 1 " model vdw 2.133 2.440 ... (remaining 149293 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 10 through 347) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 1 through 105) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 2 through 117) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.420 Check model and map are aligned: 0.280 Set scattering table: 0.180 Process input model: 47.860 Find NCS groups from input model: 0.920 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: 0.000 Load rotamer database and sin/cos tables:10.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 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 0.117 17899 Z= 0.303 Angle : 0.798 32.921 24346 Z= 0.351 Chirality : 0.050 0.815 2807 Planarity : 0.007 0.288 2991 Dihedral : 14.437 107.412 6767 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % 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: 0.66 (0.18), residues: 2103 helix: 2.10 (0.21), residues: 566 sheet: 0.17 (0.20), residues: 634 loop : -0.37 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 237 HIS 0.006 0.001 HIS D 102 PHE 0.019 0.001 PHE D 226 TYR 0.017 0.001 TYR C 157 ARG 0.003 0.000 ARG C 321 *********************** 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 386 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 386 time to evaluate : 1.899 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 232 LEU cc_start: 0.8723 (mm) cc_final: 0.8520 (mm) REVERT: B 266 MET cc_start: 0.8681 (mmm) cc_final: 0.8472 (mmm) REVERT: C 321 ARG cc_start: 0.6550 (ttm-80) cc_final: 0.6012 (ttm110) REVERT: K 90 ASP cc_start: 0.8586 (m-30) cc_final: 0.8348 (m-30) REVERT: K 98 ARG cc_start: 0.8151 (ttp80) cc_final: 0.7936 (ttt-90) outliers start: 0 outliers final: 1 residues processed: 386 average time/residue: 1.2606 time to fit residues: 543.1259 Evaluate side-chains 315 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 314 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 275 ILE 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: 3.9990 chunk 53 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 162 optimal weight: 0.3980 chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 0.7980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN B 229 GLN C 224 GLN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 HIS D 308 ASN K 28 ASN K 43 GLN K 77 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 17899 Z= 0.316 Angle : 0.642 11.276 24346 Z= 0.325 Chirality : 0.046 0.309 2807 Planarity : 0.004 0.051 2991 Dihedral : 9.367 81.860 2829 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.02 % Allowed : 11.47 % Favored : 86.51 % 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: 0.68 (0.19), residues: 2103 helix: 2.07 (0.22), residues: 566 sheet: 0.22 (0.20), residues: 640 loop : -0.36 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 47 HIS 0.007 0.001 HIS D 102 PHE 0.020 0.002 PHE E 299 TYR 0.017 0.002 TYR A 157 ARG 0.005 0.000 ARG E 194 *********************** 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 370 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 332 time to evaluate : 1.952 Fit side-chains revert: symmetry clash REVERT: A 68 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7639 (ttt90) REVERT: A 103 LYS cc_start: 0.8398 (ptmm) cc_final: 0.7983 (tttp) REVERT: A 286 MET cc_start: 0.7433 (mmp) cc_final: 0.7163 (mmm) REVERT: A 294 MET cc_start: 0.7776 (mmm) cc_final: 0.7563 (mmt) REVERT: B 93 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8493 (mptp) REVERT: B 232 LEU cc_start: 0.8780 (mm) cc_final: 0.8501 (mm) REVERT: C 286 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7124 (mtp) REVERT: C 321 ARG cc_start: 0.6619 (ttm-80) cc_final: 0.6063 (ttm110) REVERT: E 247 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8813 (mp) REVERT: E 348 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6762 (tm) outliers start: 38 outliers final: 20 residues processed: 347 average time/residue: 1.2336 time to fit residues: 479.2196 Evaluate side-chains 332 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 307 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 7 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 156 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 51 optimal weight: 0.6980 chunk 188 optimal weight: 0.8980 chunk 203 optimal weight: 7.9990 chunk 167 optimal weight: 8.9990 chunk 186 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 151 optimal weight: 0.3980 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 HIS E 152 GLN K 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 17899 Z= 0.287 Angle : 0.609 9.436 24346 Z= 0.308 Chirality : 0.045 0.272 2807 Planarity : 0.004 0.048 2991 Dihedral : 7.698 81.487 2829 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.76 % Allowed : 14.66 % Favored : 82.58 % 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: 0.61 (0.19), residues: 2103 helix: 1.88 (0.22), residues: 579 sheet: 0.28 (0.20), residues: 628 loop : -0.42 (0.21), residues: 896 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 103 HIS 0.004 0.001 HIS D 102 PHE 0.014 0.002 PHE B 258 TYR 0.023 0.002 TYR L 49 ARG 0.006 0.000 ARG I 61 *********************** 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 374 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 322 time to evaluate : 2.003 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7646 (ttt90) REVERT: A 103 LYS cc_start: 0.8391 (ptmm) cc_final: 0.8033 (tttp) REVERT: A 294 MET cc_start: 0.7803 (mmm) cc_final: 0.7591 (mmt) REVERT: A 304 TYR cc_start: 0.7237 (t80) cc_final: 0.6941 (t80) REVERT: B 112 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8287 (tpp) REVERT: B 232 LEU cc_start: 0.8747 (mm) cc_final: 0.8467 (mm) REVERT: C 286 MET cc_start: 0.7565 (OUTLIER) cc_final: 0.7053 (mtp) REVERT: C 321 ARG cc_start: 0.6673 (ttm-80) cc_final: 0.6128 (ttm110) REVERT: E 247 ILE cc_start: 0.9001 (OUTLIER) cc_final: 0.8766 (mp) REVERT: E 348 LEU cc_start: 0.7129 (OUTLIER) cc_final: 0.6809 (tm) REVERT: J 110 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8534 (pt0) REVERT: L 70 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7606 (m-30) REVERT: L 79 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.7040 (mm110) outliers start: 52 outliers final: 29 residues processed: 346 average time/residue: 1.1867 time to fit residues: 464.7645 Evaluate side-chains 339 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 302 time to evaluate : 2.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 21 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 10.0000 chunk 141 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 179 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 265 ASN C 267 HIS D 88 ASN E 152 GLN E 318 HIS K 28 ASN K 43 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 17899 Z= 0.406 Angle : 0.665 11.018 24346 Z= 0.335 Chirality : 0.047 0.297 2807 Planarity : 0.005 0.048 2991 Dihedral : 7.065 82.158 2829 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.66 % Allowed : 15.56 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.18), residues: 2103 helix: 1.68 (0.22), residues: 579 sheet: 0.21 (0.20), residues: 626 loop : -0.48 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 47 HIS 0.005 0.001 HIS D 102 PHE 0.024 0.002 PHE E 299 TYR 0.023 0.002 TYR A 157 ARG 0.006 0.001 ARG E 194 *********************** 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 386 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 317 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7701 (ttt90) REVERT: A 103 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8136 (tttp) REVERT: B 93 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8521 (mptp) REVERT: B 112 MET cc_start: 0.8706 (OUTLIER) cc_final: 0.8352 (tpp) REVERT: B 232 LEU cc_start: 0.8721 (mm) cc_final: 0.8467 (mm) REVERT: C 207 ARG cc_start: 0.8709 (OUTLIER) cc_final: 0.7806 (ttp80) REVERT: C 286 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.7121 (mtp) REVERT: C 321 ARG cc_start: 0.6671 (ttm-80) cc_final: 0.6072 (ttm110) REVERT: E 168 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7730 (mt-10) REVERT: E 247 ILE cc_start: 0.9022 (OUTLIER) cc_final: 0.8776 (mp) REVERT: E 348 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6814 (tm) REVERT: I 79 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.6616 (mm-40) REVERT: J 90 ASP cc_start: 0.7936 (m-30) cc_final: 0.7700 (m-30) REVERT: J 110 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8517 (pt0) REVERT: K 39 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.8247 (tt0) REVERT: K 67 LYS cc_start: 0.7724 (tptm) cc_final: 0.7513 (tptm) REVERT: K 91 THR cc_start: 0.8266 (OUTLIER) cc_final: 0.7909 (t) outliers start: 69 outliers final: 38 residues processed: 355 average time/residue: 1.1561 time to fit residues: 462.1876 Evaluate side-chains 354 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 304 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 207 ARG Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 21 ARG Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 39 GLN Chi-restraints excluded: chain K residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 30.0000 chunk 113 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 148 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 170 optimal weight: 3.9990 chunk 138 optimal weight: 0.0970 chunk 0 optimal weight: 7.9990 chunk 102 optimal weight: 0.7980 chunk 179 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 265 ASN C 267 HIS E 69 ASN E 152 GLN J 28 ASN K 28 ASN K 43 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17899 Z= 0.186 Angle : 0.568 12.992 24346 Z= 0.285 Chirality : 0.042 0.219 2807 Planarity : 0.004 0.044 2991 Dihedral : 6.311 80.800 2829 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.45 % Allowed : 16.73 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.18), residues: 2103 helix: 1.82 (0.22), residues: 581 sheet: 0.29 (0.20), residues: 616 loop : -0.37 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 237 HIS 0.005 0.001 HIS C 267 PHE 0.016 0.001 PHE C 289 TYR 0.027 0.001 TYR L 49 ARG 0.005 0.000 ARG I 18 *********************** 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 386 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 321 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7587 (ttt90) REVERT: A 103 LYS cc_start: 0.8367 (ptmm) cc_final: 0.7993 (tttp) REVERT: A 304 TYR cc_start: 0.7241 (t80) cc_final: 0.7013 (t80) REVERT: B 112 MET cc_start: 0.8714 (OUTLIER) cc_final: 0.8268 (tpp) REVERT: C 138 MET cc_start: 0.8945 (mtt) cc_final: 0.8471 (mtt) REVERT: C 286 MET cc_start: 0.7602 (OUTLIER) cc_final: 0.7096 (mtp) REVERT: C 321 ARG cc_start: 0.6512 (ttm-80) cc_final: 0.6031 (ttm110) REVERT: E 247 ILE cc_start: 0.8926 (OUTLIER) cc_final: 0.8652 (mp) REVERT: E 348 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6852 (tm) REVERT: I 79 GLN cc_start: 0.7629 (OUTLIER) cc_final: 0.6693 (mm-40) REVERT: I 104 GLU cc_start: 0.5002 (OUTLIER) cc_final: 0.4073 (tt0) REVERT: J 90 ASP cc_start: 0.7981 (m-30) cc_final: 0.7716 (m-30) REVERT: J 110 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8523 (pt0) REVERT: K 67 LYS cc_start: 0.7728 (tptm) cc_final: 0.7465 (tptm) outliers start: 65 outliers final: 26 residues processed: 357 average time/residue: 1.1748 time to fit residues: 472.3503 Evaluate side-chains 335 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 301 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 117 optimal weight: 0.0870 chunk 49 optimal weight: 0.7980 chunk 200 optimal weight: 7.9990 chunk 166 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 overall best weight: 2.9764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** C 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 267 HIS E 152 GLN J 28 ASN K 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 17899 Z= 0.362 Angle : 0.644 15.486 24346 Z= 0.323 Chirality : 0.046 0.253 2807 Planarity : 0.004 0.046 2991 Dihedral : 6.430 82.850 2829 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 4.14 % Allowed : 18.06 % Favored : 77.80 % 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: 0.51 (0.18), residues: 2103 helix: 1.70 (0.22), residues: 579 sheet: 0.28 (0.20), residues: 624 loop : -0.45 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 237 HIS 0.005 0.001 HIS C 267 PHE 0.025 0.002 PHE D 304 TYR 0.025 0.002 TYR C 299 ARG 0.006 0.000 ARG I 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 307 time to evaluate : 2.347 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8131 (tpp) cc_final: 0.7846 (tpt) REVERT: A 68 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7703 (ttt90) REVERT: A 84 ASP cc_start: 0.7801 (OUTLIER) cc_final: 0.7583 (t0) REVERT: A 103 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.8112 (tttp) REVERT: A 304 TYR cc_start: 0.7235 (t80) cc_final: 0.6982 (t80) REVERT: B 112 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8397 (tpp) REVERT: C 231 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8152 (mp) REVERT: C 286 MET cc_start: 0.7633 (OUTLIER) cc_final: 0.7119 (mtp) REVERT: C 321 ARG cc_start: 0.6630 (ttm-80) cc_final: 0.6040 (ttm110) REVERT: C 333 ILE cc_start: 0.8788 (OUTLIER) cc_final: 0.8528 (mm) REVERT: E 68 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8667 (mp) REVERT: E 168 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7715 (mt-10) REVERT: E 247 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8705 (mp) REVERT: E 348 LEU cc_start: 0.7117 (OUTLIER) cc_final: 0.6785 (tm) REVERT: I 79 GLN cc_start: 0.7704 (OUTLIER) cc_final: 0.6808 (mm-40) REVERT: I 104 GLU cc_start: 0.5074 (OUTLIER) cc_final: 0.3743 (tm-30) REVERT: J 110 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8482 (pt0) REVERT: L 79 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7174 (mm110) outliers start: 78 outliers final: 44 residues processed: 352 average time/residue: 1.1192 time to fit residues: 445.6501 Evaluate side-chains 357 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 299 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 110 GLN Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 21 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 111 optimal weight: 2.9990 chunk 199 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 265 ASN C 267 HIS E 69 ASN E 152 GLN J 28 ASN K 43 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17899 Z= 0.263 Angle : 0.606 16.737 24346 Z= 0.303 Chirality : 0.044 0.216 2807 Planarity : 0.004 0.044 2991 Dihedral : 6.293 82.359 2829 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.93 % Allowed : 18.53 % Favored : 77.54 % 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: 0.50 (0.18), residues: 2103 helix: 1.70 (0.22), residues: 579 sheet: 0.23 (0.20), residues: 626 loop : -0.41 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 237 HIS 0.005 0.001 HIS C 267 PHE 0.024 0.002 PHE E 299 TYR 0.030 0.002 TYR C 299 ARG 0.010 0.000 ARG I 18 *********************** 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 384 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 310 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8099 (tpp) cc_final: 0.7758 (tpt) REVERT: A 68 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.7666 (ttt90) REVERT: A 103 LYS cc_start: 0.8408 (ptmm) cc_final: 0.8074 (tttp) REVERT: A 304 TYR cc_start: 0.7255 (t80) cc_final: 0.7020 (t80) REVERT: B 93 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8520 (mptp) REVERT: B 112 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8308 (tpp) REVERT: C 231 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8063 (mp) REVERT: C 286 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7091 (mtp) REVERT: C 321 ARG cc_start: 0.6611 (ttm-80) cc_final: 0.6032 (ttm110) REVERT: C 333 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8522 (mm) REVERT: E 68 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8638 (mp) REVERT: E 168 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7667 (mt-10) REVERT: E 247 ILE cc_start: 0.8958 (OUTLIER) cc_final: 0.8693 (mp) REVERT: E 348 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6729 (tm) REVERT: I 79 GLN cc_start: 0.7698 (OUTLIER) cc_final: 0.6793 (mm-40) REVERT: I 104 GLU cc_start: 0.4936 (OUTLIER) cc_final: 0.3950 (tt0) REVERT: K 39 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8350 (tt0) outliers start: 74 outliers final: 41 residues processed: 356 average time/residue: 1.1846 time to fit residues: 474.1495 Evaluate side-chains 350 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 297 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 22 SER Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 39 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 60 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 38 optimal weight: 1.9990 chunk 126 optimal weight: 0.0980 chunk 135 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 265 ASN C 267 HIS D 204 GLN E 69 ASN E 152 GLN J 28 ASN K 43 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17899 Z= 0.240 Angle : 0.597 17.139 24346 Z= 0.297 Chirality : 0.043 0.197 2807 Planarity : 0.004 0.044 2991 Dihedral : 6.206 82.092 2829 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.93 % Allowed : 18.85 % Favored : 77.22 % 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: 0.55 (0.18), residues: 2103 helix: 1.71 (0.22), residues: 579 sheet: 0.25 (0.20), residues: 636 loop : -0.37 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 237 HIS 0.006 0.001 HIS C 267 PHE 0.027 0.002 PHE D 304 TYR 0.036 0.001 TYR C 299 ARG 0.007 0.000 ARG I 18 *********************** 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 381 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 307 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8087 (tpp) cc_final: 0.7718 (tpt) REVERT: A 68 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7625 (ttt90) REVERT: A 84 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7572 (t0) REVERT: A 103 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8051 (tttp) REVERT: A 304 TYR cc_start: 0.7257 (t80) cc_final: 0.6992 (t80) REVERT: B 93 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8527 (mptp) REVERT: B 112 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8356 (tpp) REVERT: C 231 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8135 (mp) REVERT: C 286 MET cc_start: 0.7644 (OUTLIER) cc_final: 0.7090 (mtp) REVERT: C 321 ARG cc_start: 0.6603 (ttm-80) cc_final: 0.6033 (ttm110) REVERT: C 333 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8550 (mm) REVERT: E 68 ILE cc_start: 0.8911 (OUTLIER) cc_final: 0.8616 (mp) REVERT: E 168 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7650 (mt-10) REVERT: E 247 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8680 (mp) REVERT: E 348 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6761 (tm) REVERT: I 79 GLN cc_start: 0.7708 (OUTLIER) cc_final: 0.6836 (mm-40) REVERT: I 104 GLU cc_start: 0.4899 (OUTLIER) cc_final: 0.3935 (tt0) outliers start: 74 outliers final: 43 residues processed: 352 average time/residue: 1.2011 time to fit residues: 475.5896 Evaluate side-chains 351 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 295 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 302 ILE Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 88 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 21 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 7.9990 chunk 191 optimal weight: 10.0000 chunk 174 optimal weight: 0.7980 chunk 185 optimal weight: 0.6980 chunk 111 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 168 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 267 HIS E 152 GLN J 28 ASN K 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17899 Z= 0.236 Angle : 0.601 17.360 24346 Z= 0.298 Chirality : 0.043 0.194 2807 Planarity : 0.004 0.044 2991 Dihedral : 6.203 81.941 2829 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 3.40 % Allowed : 19.76 % Favored : 76.85 % 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: 0.54 (0.18), residues: 2103 helix: 1.68 (0.22), residues: 579 sheet: 0.26 (0.20), residues: 635 loop : -0.37 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 237 HIS 0.007 0.001 HIS C 267 PHE 0.029 0.002 PHE D 304 TYR 0.048 0.001 TYR C 299 ARG 0.007 0.000 ARG I 18 *********************** 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 368 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 304 time to evaluate : 2.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8069 (tpp) cc_final: 0.7735 (tpt) REVERT: A 68 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.7636 (ttt90) REVERT: A 84 ASP cc_start: 0.7805 (OUTLIER) cc_final: 0.7582 (t0) REVERT: A 103 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.8049 (tttp) REVERT: A 297 LEU cc_start: 0.7848 (OUTLIER) cc_final: 0.7347 (tm) REVERT: A 304 TYR cc_start: 0.7267 (t80) cc_final: 0.7011 (t80) REVERT: B 93 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8528 (mptp) REVERT: B 112 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8336 (tpp) REVERT: C 40 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8236 (mtm) REVERT: C 231 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.8035 (mp) REVERT: C 286 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7103 (mtp) REVERT: C 321 ARG cc_start: 0.6625 (ttm-80) cc_final: 0.6053 (ttm110) REVERT: C 333 ILE cc_start: 0.8781 (OUTLIER) cc_final: 0.8544 (mm) REVERT: E 68 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8627 (mp) REVERT: E 168 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7642 (mt-10) REVERT: E 247 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8683 (mp) REVERT: E 348 LEU cc_start: 0.7123 (OUTLIER) cc_final: 0.6780 (tm) REVERT: I 79 GLN cc_start: 0.7690 (OUTLIER) cc_final: 0.6809 (mm-40) REVERT: I 104 GLU cc_start: 0.4830 (OUTLIER) cc_final: 0.3881 (tt0) outliers start: 64 outliers final: 42 residues processed: 340 average time/residue: 1.1727 time to fit residues: 448.7909 Evaluate side-chains 355 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 298 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 21 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 136 optimal weight: 1.9990 chunk 206 optimal weight: 3.9990 chunk 189 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 100 optimal weight: 0.0870 chunk 130 optimal weight: 5.9990 overall best weight: 1.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 267 HIS E 152 GLN J 28 ASN J 65 GLN K 43 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17899 Z= 0.249 Angle : 0.609 17.358 24346 Z= 0.301 Chirality : 0.043 0.192 2807 Planarity : 0.004 0.044 2991 Dihedral : 6.225 82.327 2829 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.40 % Allowed : 20.13 % Favored : 76.47 % 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: 0.51 (0.18), residues: 2103 helix: 1.64 (0.22), residues: 579 sheet: 0.26 (0.20), residues: 635 loop : -0.39 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 237 HIS 0.008 0.001 HIS C 267 PHE 0.032 0.002 PHE D 304 TYR 0.047 0.002 TYR C 299 ARG 0.007 0.000 ARG I 18 ********************** 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 369 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 305 time to evaluate : 2.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.8055 (tpp) cc_final: 0.7697 (tpt) REVERT: A 53 VAL cc_start: 0.8933 (m) cc_final: 0.8728 (t) REVERT: A 68 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7628 (ttt90) REVERT: A 84 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7587 (t0) REVERT: A 103 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8052 (tttp) REVERT: A 297 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7344 (tm) REVERT: A 304 TYR cc_start: 0.7275 (t80) cc_final: 0.7010 (t80) REVERT: B 93 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8529 (mptp) REVERT: B 112 MET cc_start: 0.8743 (OUTLIER) cc_final: 0.8346 (tpp) REVERT: C 40 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8244 (mtm) REVERT: C 231 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8101 (mp) REVERT: C 286 MET cc_start: 0.7632 (OUTLIER) cc_final: 0.7111 (mtp) REVERT: C 321 ARG cc_start: 0.6615 (ttm-80) cc_final: 0.6035 (ttm110) REVERT: C 333 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8560 (mm) REVERT: E 68 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8630 (mp) REVERT: E 168 GLU cc_start: 0.7875 (mt-10) cc_final: 0.7654 (mt-10) REVERT: E 247 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8680 (mp) REVERT: E 348 LEU cc_start: 0.7105 (OUTLIER) cc_final: 0.6762 (tm) REVERT: I 79 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.6851 (mm-40) REVERT: I 104 GLU cc_start: 0.4770 (OUTLIER) cc_final: 0.3812 (tt0) REVERT: L 13 MET cc_start: 0.5278 (ppp) cc_final: 0.4969 (ppp) outliers start: 64 outliers final: 44 residues processed: 342 average time/residue: 1.1581 time to fit residues: 447.6117 Evaluate side-chains 356 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 297 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ARG Chi-restraints excluded: chain A residue 84 ASP Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 171 ASP Chi-restraints excluded: chain A residue 173 ASN Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 43 THR Chi-restraints excluded: chain B residue 93 LYS Chi-restraints excluded: chain B residue 112 MET Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 298 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 40 MET Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain C residue 131 THR Chi-restraints excluded: chain C residue 165 GLU Chi-restraints excluded: chain C residue 227 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 286 MET Chi-restraints excluded: chain C residue 323 PHE Chi-restraints excluded: chain C residue 333 ILE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 236 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 247 ILE Chi-restraints excluded: chain E residue 300 VAL Chi-restraints excluded: chain E residue 348 LEU Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 82 ASP Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain I residue 104 GLU Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 76 SER Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 114 VAL Chi-restraints excluded: chain J residue 115 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 15 VAL Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 21 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.8980 chunk 50 optimal weight: 0.0470 chunk 151 optimal weight: 0.1980 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 chunk 168 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 30 optimal weight: 30.0000 chunk 144 optimal weight: 6.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 267 HIS E 152 GLN J 28 ASN K 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.130928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.091888 restraints weight = 24169.520| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.99 r_work: 0.2956 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 17899 Z= 0.159 Angle : 0.566 17.160 24346 Z= 0.279 Chirality : 0.042 0.187 2807 Planarity : 0.004 0.043 2991 Dihedral : 5.867 80.572 2829 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.55 % Allowed : 20.92 % Favored : 76.53 % 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: 0.66 (0.19), residues: 2103 helix: 1.76 (0.22), residues: 577 sheet: 0.35 (0.20), residues: 626 loop : -0.29 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 237 HIS 0.008 0.001 HIS C 267 PHE 0.030 0.002 PHE D 304 TYR 0.040 0.001 TYR C 299 ARG 0.007 0.000 ARG I 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7433.97 seconds wall clock time: 132 minutes 26.72 seconds (7946.72 seconds total)