Starting phenix.real_space_refine on Sun Mar 17 10:11:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x40_22038/03_2024/6x40_22038_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x40_22038/03_2024/6x40_22038.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x40_22038/03_2024/6x40_22038.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x40_22038/03_2024/6x40_22038.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x40_22038/03_2024/6x40_22038_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x40_22038/03_2024/6x40_22038_updated.pdb" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 11240 2.51 5 N 2829 2.21 5 O 3245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B GLU 209": "OE1" <-> "OE2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C ARG 318": "NH1" <-> "NH2" Residue "C ARG 321": "NH1" <-> "NH2" Residue "D ARG 17": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D ARG 173": "NH1" <-> "NH2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D GLU 303": "OE1" <-> "OE2" 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 GLU 162": "OE1" <-> "OE2" Residue "E ARG 176": "NH1" <-> "NH2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E ARG 197": "NH1" <-> "NH2" Residue "E ARG 207": "NH1" <-> "NH2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "E GLU 313": "OE1" <-> "OE2" Residue "E ARG 327": "NH1" <-> "NH2" Residue "I TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "J ARG 102": "NH1" <-> "NH2" Residue "L GLU 41": "OE1" <-> "OE2" Residue "K TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K ARG 98": "NH1" <-> "NH2" Residue "K ARG 102": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17411 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: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'RI5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.63, per 1000 atoms: 0.55 Number of scatterers: 17411 At special positions: 0 Unit cell: (129.525, 139.425, 122.1, 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 3245 8.00 N 2829 7.00 C 11240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.04 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " " MAN G 8 " - " MAN G 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 10 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 404 " - " ASN A 80 " " NAG C 404 " - " ASN C 80 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN D 111 " " NAG N 1 " - " ASN E 208 " Time building additional restraints: 6.97 Conformation dependent library (CDL) restraints added in 2.9 seconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 37 helices and 27 sheets defined 28.1% alpha, 28.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.03 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 Processing helix chain 'A' and resid 70 through 72 No H-bonds generated for 'chain 'A' and resid 70 through 72' Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 140 through 142 No H-bonds generated for 'chain 'A' and resid 140 through 142' Processing helix chain 'A' and resid 219 through 241 removed outlier: 3.914A pdb=" N LEU A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N MET A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix removed outlier: 4.583A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 269 Processing helix chain 'A' and resid 280 through 304 Processing helix chain 'A' and resid 310 through 338 removed outlier: 3.586A pdb=" N ALA A 314 " --> pdb=" O PRO A 310 " (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 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 224 through 246 removed outlier: 3.998A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LEU B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix removed outlier: 4.165A pdb=" N SER B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TRP B 246 " --> pdb=" O GLN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 275 removed outlier: 4.237A pdb=" N ASN B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 309 Processing helix chain 'B' and resid 315 through 344 removed outlier: 4.163A pdb=" N ALA B 319 " --> pdb=" O PRO B 315 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 219 through 241 removed outlier: 5.194A pdb=" N MET C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix removed outlier: 3.691A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 267 Processing helix chain 'C' and resid 280 through 304 Processing helix chain 'C' and resid 310 through 338 removed outlier: 3.598A pdb=" N ILE C 322 " --> pdb=" O ARG C 318 " (cutoff:3.500A) Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 224 through 246 removed outlier: 3.776A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N LEU D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Proline residue: D 233 - end of helix removed outlier: 4.233A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TRP D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 274 Processing helix chain 'D' and resid 285 through 310 Processing helix chain 'D' and resid 315 through 345 removed outlier: 3.731A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N PHE D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Proline residue: D 330 - end of helix Processing helix chain 'E' and resid 27 through 34 Processing helix chain 'E' and resid 100 through 105 removed outlier: 4.443A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 256 removed outlier: 5.623A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix removed outlier: 3.627A pdb=" N VAL E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N SER E 254 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N PHE E 255 " --> pdb=" O SER E 251 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TRP E 256 " --> pdb=" O TRP E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 285 removed outlier: 3.660A pdb=" N THR E 281 " --> pdb=" O THR E 277 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 323 removed outlier: 4.348A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 329 Processing helix chain 'E' and resid 331 through 356 removed outlier: 3.942A pdb=" N ILE E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) Proline residue: E 340 - end of helix Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'A' and resid 164 through 168 removed outlier: 6.319A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.513A 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: 3.700A pdb=" N CYS A 150 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.684A 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: 6.758A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.839A 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: 6.191A pdb=" N THR B 39 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N GLU B 170 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL B 41 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 4.134A 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: 4.088A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU B 193 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.356A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU C 83 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.683A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.924A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 167 through 171 removed outlier: 6.413A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 45 through 47 Processing sheet with id= L, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= M, first strand: chain 'D' and resid 150 through 154 removed outlier: 3.975A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 179 through 183 removed outlier: 5.758A pdb=" N THR E 51 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLN E 182 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N ILE E 53 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 188 through 190 removed outlier: 6.597A pdb=" N MET E 57 " --> pdb=" O GLU E 189 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.682A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 116 through 121 removed outlier: 6.904A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 4 through 7 Processing sheet with id= S, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.935A pdb=" N LYS I 102 " --> pdb=" O MET I 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'I' and resid 85 through 90 removed outlier: 6.261A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 3 through 6 Processing sheet with id= V, first strand: chain 'J' and resid 10 through 12 removed outlier: 6.205A pdb=" N LYS J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N TRP J 47 " --> pdb=" O LYS J 38 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= X, first strand: chain 'L' and resid 85 through 90 removed outlier: 6.282A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 3 through 6 Processing sheet with id= Z, first strand: chain 'K' and resid 10 through 12 Processing sheet with id= AA, first strand: chain 'K' and resid 58 through 60 removed outlier: 6.842A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N TYR K 33 " --> pdb=" O LYS K 99 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 730 hydrogen bonds defined for protein. 2127 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: 5.59 Time building geometry restraints manager: 7.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 3478 1.33 - 1.45: 5299 1.45 - 1.58: 8905 1.58 - 1.71: 0 1.71 - 1.84: 167 Bond restraints: 17849 Sorted by residual: bond pdb=" CD ABU A 405 " pdb=" OE1 ABU A 405 " ideal model delta sigma weight residual 1.247 1.334 -0.087 2.00e-02 2.50e+03 1.87e+01 bond pdb=" CD ABU C 405 " pdb=" OE2 ABU C 405 " ideal model delta sigma weight residual 1.250 1.334 -0.084 2.00e-02 2.50e+03 1.78e+01 bond pdb=" N SER E 286 " pdb=" CA SER E 286 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.17e-02 7.31e+03 9.18e+00 bond pdb=" N ASN A 100 " pdb=" CA ASN A 100 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.10e-02 8.26e+03 8.28e+00 bond pdb=" N LYS E 184 " pdb=" CA LYS E 184 " ideal model delta sigma weight residual 1.452 1.488 -0.037 1.30e-02 5.92e+03 7.97e+00 ... (remaining 17844 not shown) Histogram of bond angle deviations from ideal: 59.34 - 74.62: 3 74.62 - 89.91: 0 89.91 - 105.19: 372 105.19 - 120.47: 16866 120.47 - 135.75: 7043 Bond angle restraints: 24284 Sorted by residual: angle pdb=" CA LEU K 11 " pdb=" CB LEU K 11 " pdb=" CG LEU K 11 " ideal model delta sigma weight residual 116.30 135.75 -19.45 3.50e+00 8.16e-02 3.09e+01 angle pdb=" CA LEU B 277 " pdb=" CB LEU B 277 " pdb=" CG LEU B 277 " ideal model delta sigma weight residual 116.30 135.13 -18.83 3.50e+00 8.16e-02 2.89e+01 angle pdb=" CA MET C 227 " pdb=" CB MET C 227 " pdb=" CG MET C 227 " ideal model delta sigma weight residual 114.10 123.90 -9.80 2.00e+00 2.50e-01 2.40e+01 angle pdb=" CB MET I 11 " pdb=" CG MET I 11 " pdb=" SD MET I 11 " ideal model delta sigma weight residual 112.70 99.06 13.64 3.00e+00 1.11e-01 2.07e+01 angle pdb=" CA MET A 227 " pdb=" CB MET A 227 " pdb=" CG MET A 227 " ideal model delta sigma weight residual 114.10 123.08 -8.98 2.00e+00 2.50e-01 2.02e+01 ... (remaining 24279 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.86: 10216 21.86 - 43.72: 545 43.72 - 65.58: 54 65.58 - 87.44: 40 87.44 - 109.29: 16 Dihedral angle restraints: 10871 sinusoidal: 4615 harmonic: 6256 Sorted by residual: dihedral pdb=" CB CYS A 136 " pdb=" SG CYS A 136 " pdb=" SG CYS A 150 " pdb=" CB CYS A 150 " ideal model delta sinusoidal sigma weight residual -86.00 -8.68 -77.32 1 1.00e+01 1.00e-02 7.49e+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 -86.00 -9.99 -76.01 1 1.00e+01 1.00e-02 7.28e+01 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 -11.23 -74.77 1 1.00e+01 1.00e-02 7.08e+01 ... (remaining 10868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.761: 2809 0.761 - 1.521: 2 1.521 - 2.282: 0 2.282 - 3.043: 1 3.043 - 3.803: 2 Chirality restraints: 2814 Sorted by residual: chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 1.40 -3.80 2.00e-02 2.50e+03 3.62e+04 chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 0.85 -3.25 2.00e-02 2.50e+03 2.63e+04 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 0.08 -2.48 2.00e-02 2.50e+03 1.54e+04 ... (remaining 2811 not shown) Planarity restraints: 2992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " -0.196 2.00e-02 2.50e+03 1.66e-01 3.44e+02 pdb=" C7 NAG N 1 " 0.040 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.039 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " 0.270 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " -0.153 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " 0.192 2.00e-02 2.50e+03 1.59e-01 3.15e+02 pdb=" C7 NAG N 2 " -0.052 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " 0.140 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " -0.257 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " 0.129 2.00e-02 2.50e+03 1.06e-01 1.41e+02 pdb=" C7 NAG G 2 " -0.035 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " 0.096 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " -0.171 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " -0.020 2.00e-02 2.50e+03 ... (remaining 2989 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3040 2.77 - 3.30: 15384 3.30 - 3.83: 29964 3.83 - 4.37: 36297 4.37 - 4.90: 62956 Nonbonded interactions: 147641 Sorted by model distance: nonbonded pdb=" OE1 GLN C 224 " pdb=" OG1 THR C 225 " model vdw 2.233 2.440 nonbonded pdb=" O ALA C 252 " pdb=" OG1 THR C 256 " model vdw 2.243 2.440 nonbonded pdb=" OD2 ASP A 121 " pdb=" OG1 THR A 123 " model vdw 2.288 2.440 nonbonded pdb=" OG SER A 247 " pdb=" OG SER B 251 " model vdw 2.290 2.440 nonbonded pdb=" OH TYR D 26 " pdb=" OD2 ASP D 72 " model vdw 2.294 2.440 ... (remaining 147636 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 10 through 347) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 1 through 105) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 2 through 117) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.990 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: 5.840 Check model and map are aligned: 0.260 Set scattering table: 0.170 Process input model: 47.300 Find NCS groups from input model: 1.080 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 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 : 0.008 0.087 17849 Z= 0.493 Angle : 1.123 19.449 24284 Z= 0.589 Chirality : 0.131 3.803 2814 Planarity : 0.008 0.166 2985 Dihedral : 14.332 109.295 6824 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.42 % Allowed : 6.27 % Favored : 93.31 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.03 (0.16), residues: 2103 helix: -0.26 (0.20), residues: 564 sheet: -0.88 (0.18), residues: 627 loop : -2.36 (0.17), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 336 HIS 0.008 0.001 HIS C 267 PHE 0.060 0.003 PHE B 258 TYR 0.039 0.003 TYR C 157 ARG 0.006 0.001 ARG K 98 *********************** 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 460 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 452 time to evaluate : 2.058 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.7199 (ptp) cc_final: 0.6692 (pp-130) REVERT: A 153 GLU cc_start: 0.8542 (mm-30) cc_final: 0.8315 (mm-30) REVERT: B 138 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7483 (mt-10) REVERT: B 209 GLU cc_start: 0.7489 (mt-10) cc_final: 0.7083 (mt-10) REVERT: B 236 MET cc_start: 0.6708 (mmp) cc_final: 0.6390 (mmp) REVERT: C 43 ASP cc_start: 0.7897 (m-30) cc_final: 0.7573 (m-30) REVERT: C 163 ASP cc_start: 0.8278 (m-30) cc_final: 0.7971 (m-30) REVERT: C 227 MET cc_start: 0.6835 (mmm) cc_final: 0.6270 (ptm) REVERT: D 123 GLU cc_start: 0.7607 (pt0) cc_final: 0.7330 (pm20) REVERT: D 192 ASP cc_start: 0.7641 (t0) cc_final: 0.7441 (t0) REVERT: E 68 ILE cc_start: 0.8856 (mt) cc_final: 0.8572 (mm) REVERT: L 11 MET cc_start: 0.6305 (ptp) cc_final: 0.6039 (ptm) REVERT: K 46 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6797 (mt-10) outliers start: 8 outliers final: 4 residues processed: 457 average time/residue: 1.1923 time to fit residues: 611.5905 Evaluate side-chains 354 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 350 time to evaluate : 1.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain D residue 55 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 105 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 162 optimal weight: 0.0570 chunk 62 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 10.0000 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 65 GLN A 185 GLN A 224 GLN A 265 ASN B 68 GLN B 229 GLN B 275 ASN B 308 ASN B 346 ASN C 65 GLN C 185 GLN C 265 ASN C 267 HIS C 303 ASN D 68 GLN D 88 ASN D 102 HIS D 189 ASN D 275 ASN D 314 GLN D 337 ASN E 69 ASN E 80 GLN E 128 ASN E 163 HIS I 53 ASN J 6 GLN L 53 ASN K 6 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 17849 Z= 0.202 Angle : 0.606 10.333 24284 Z= 0.301 Chirality : 0.045 0.261 2814 Planarity : 0.004 0.060 2985 Dihedral : 8.579 77.932 2891 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.25 % Allowed : 15.45 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.17), residues: 2103 helix: 0.25 (0.21), residues: 561 sheet: -0.76 (0.19), residues: 638 loop : -1.75 (0.18), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 103 HIS 0.002 0.001 HIS C 107 PHE 0.012 0.001 PHE B 310 TYR 0.016 0.001 TYR C 157 ARG 0.005 0.000 ARG B 85 *********************** 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 442 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 362 time to evaluate : 2.000 Fit side-chains revert: symmetry clash REVERT: A 49 MET cc_start: 0.7205 (ptp) cc_final: 0.6603 (pp-130) REVERT: B 58 MET cc_start: 0.8151 (mtt) cc_final: 0.7925 (mtm) REVERT: B 138 GLU cc_start: 0.7663 (mt-10) cc_final: 0.7455 (mt-10) REVERT: B 190 GLN cc_start: 0.8063 (tt0) cc_final: 0.7753 (tt0) REVERT: B 236 MET cc_start: 0.6727 (mmp) cc_final: 0.6515 (mmp) REVERT: B 258 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7778 (t80) REVERT: C 43 ASP cc_start: 0.7941 (m-30) cc_final: 0.7655 (m-30) REVERT: C 227 MET cc_start: 0.7061 (mmm) cc_final: 0.6472 (ttt) REVERT: C 303 ASN cc_start: 0.7642 (t0) cc_final: 0.7326 (t0) REVERT: D 123 GLU cc_start: 0.7659 (pt0) cc_final: 0.7327 (pm20) REVERT: E 232 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.6901 (ptm-80) REVERT: E 236 PHE cc_start: 0.7601 (m-80) cc_final: 0.7338 (m-80) REVERT: E 334 TYR cc_start: 0.6795 (OUTLIER) cc_final: 0.6315 (m-10) REVERT: E 355 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7389 (mp) REVERT: I 13 MET cc_start: 0.5507 (ppp) cc_final: 0.5280 (pp-130) REVERT: I 102 LYS cc_start: 0.8467 (tptm) cc_final: 0.8258 (tptp) REVERT: J 98 ARG cc_start: 0.8502 (ttp80) cc_final: 0.7893 (ttt90) REVERT: L 11 MET cc_start: 0.6265 (ptp) cc_final: 0.6050 (ptm) REVERT: K 34 MET cc_start: 0.8811 (mmm) cc_final: 0.8588 (tpt) REVERT: K 46 GLU cc_start: 0.7268 (mt-10) cc_final: 0.6886 (mt-10) outliers start: 80 outliers final: 36 residues processed: 394 average time/residue: 1.1334 time to fit residues: 503.4806 Evaluate side-chains 380 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 340 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 209 SER Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 21 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 156 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 188 optimal weight: 0.7980 chunk 203 optimal weight: 3.9990 chunk 167 optimal weight: 5.9990 chunk 186 optimal weight: 7.9990 chunk 64 optimal weight: 0.7980 chunk 151 optimal weight: 0.0370 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 314 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17849 Z= 0.215 Angle : 0.571 11.608 24284 Z= 0.283 Chirality : 0.044 0.281 2814 Planarity : 0.004 0.058 2985 Dihedral : 6.778 66.701 2889 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.67 % Allowed : 18.27 % Favored : 77.06 % 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: -0.99 (0.17), residues: 2103 helix: 0.60 (0.21), residues: 561 sheet: -0.54 (0.19), residues: 609 loop : -1.48 (0.19), residues: 933 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 237 HIS 0.003 0.001 HIS D 218 PHE 0.017 0.001 PHE E 338 TYR 0.030 0.001 TYR E 314 ARG 0.006 0.000 ARG C 250 *********************** 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 437 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 349 time to evaluate : 2.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.7208 (ptp) cc_final: 0.6571 (pp-130) REVERT: A 224 GLN cc_start: 0.8308 (tp40) cc_final: 0.7938 (tp-100) REVERT: B 90 MET cc_start: 0.8118 (tpt) cc_final: 0.7703 (tpt) REVERT: B 138 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7493 (mt-10) REVERT: B 141 MET cc_start: 0.8758 (mtt) cc_final: 0.8503 (mtt) REVERT: B 229 GLN cc_start: 0.7403 (tp-100) cc_final: 0.7182 (tp-100) REVERT: B 258 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7956 (t80) REVERT: C 43 ASP cc_start: 0.7969 (m-30) cc_final: 0.7606 (m-30) REVERT: C 214 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8646 (mt) REVERT: C 227 MET cc_start: 0.7099 (mmm) cc_final: 0.6493 (ttt) REVERT: C 303 ASN cc_start: 0.7596 (t0) cc_final: 0.7309 (t0) REVERT: D 123 GLU cc_start: 0.7676 (pt0) cc_final: 0.7310 (pm20) REVERT: D 249 ARG cc_start: 0.7436 (mtm110) cc_final: 0.7189 (mtm110) REVERT: E 68 ILE cc_start: 0.8869 (mt) cc_final: 0.8581 (mm) REVERT: E 232 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.6934 (ptm-80) REVERT: E 272 THR cc_start: 0.8871 (t) cc_final: 0.8529 (m) REVERT: E 306 PHE cc_start: 0.7149 (m-10) cc_final: 0.6923 (m-80) REVERT: E 334 TYR cc_start: 0.6873 (OUTLIER) cc_final: 0.6337 (m-10) REVERT: E 355 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7269 (mp) REVERT: I 13 MET cc_start: 0.5467 (ppp) cc_final: 0.5199 (pp-130) REVERT: I 102 LYS cc_start: 0.8512 (tptm) cc_final: 0.8311 (tptp) REVERT: J 46 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7522 (pt0) REVERT: L 11 MET cc_start: 0.6577 (ptp) cc_final: 0.6323 (ptm) REVERT: K 13 LYS cc_start: 0.7357 (OUTLIER) cc_final: 0.6840 (mttm) REVERT: K 19 LYS cc_start: 0.8660 (tttt) cc_final: 0.8342 (tptm) REVERT: K 46 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6992 (mt-10) REVERT: K 110 GLN cc_start: 0.8043 (pt0) cc_final: 0.7841 (pm20) outliers start: 88 outliers final: 49 residues processed: 384 average time/residue: 1.1096 time to fit residues: 480.8460 Evaluate side-chains 393 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 337 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 45 LYS Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 13 LYS Chi-restraints excluded: chain K residue 17 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: 4.9990 chunk 141 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 188 optimal weight: 1.9990 chunk 200 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN C 41 ASN C 265 ASN D 314 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 17849 Z= 0.398 Angle : 0.651 10.553 24284 Z= 0.326 Chirality : 0.047 0.225 2814 Planarity : 0.005 0.059 2985 Dihedral : 6.491 58.622 2888 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 6.32 % Allowed : 18.48 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.17), residues: 2103 helix: 0.65 (0.21), residues: 567 sheet: -0.73 (0.18), residues: 649 loop : -1.16 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 237 HIS 0.005 0.001 HIS D 102 PHE 0.016 0.002 PHE B 101 TYR 0.033 0.002 TYR E 314 ARG 0.006 0.001 ARG C 250 *********************** 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 457 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 338 time to evaluate : 2.124 Fit side-chains revert: symmetry clash REVERT: A 49 MET cc_start: 0.7292 (ptp) cc_final: 0.6537 (pp-130) REVERT: A 224 GLN cc_start: 0.8351 (tp40) cc_final: 0.8024 (tp-100) REVERT: B 81 MET cc_start: 0.7326 (OUTLIER) cc_final: 0.6907 (ttp) REVERT: B 138 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7516 (mt-10) REVERT: B 141 MET cc_start: 0.8800 (mtt) cc_final: 0.8590 (mtt) REVERT: B 229 GLN cc_start: 0.7478 (tp-100) cc_final: 0.7172 (tp-100) REVERT: B 258 PHE cc_start: 0.8305 (OUTLIER) cc_final: 0.8027 (t80) REVERT: C 43 ASP cc_start: 0.8035 (m-30) cc_final: 0.7666 (m-30) REVERT: C 227 MET cc_start: 0.7298 (mmm) cc_final: 0.6714 (ttt) REVERT: C 303 ASN cc_start: 0.7586 (t0) cc_final: 0.7336 (t0) REVERT: D 123 GLU cc_start: 0.7821 (pt0) cc_final: 0.7405 (pm20) REVERT: D 170 GLU cc_start: 0.7648 (tp30) cc_final: 0.7445 (tp30) REVERT: D 249 ARG cc_start: 0.7481 (mtm110) cc_final: 0.6971 (mtp-110) REVERT: E 68 ILE cc_start: 0.9011 (mt) cc_final: 0.8739 (mm) REVERT: E 197 ARG cc_start: 0.7795 (mtp180) cc_final: 0.7352 (mtp180) REVERT: E 199 TYR cc_start: 0.7516 (m-80) cc_final: 0.7075 (m-80) REVERT: E 232 ARG cc_start: 0.8258 (OUTLIER) cc_final: 0.7004 (ptm-80) REVERT: E 236 PHE cc_start: 0.7813 (m-80) cc_final: 0.7395 (m-80) REVERT: E 331 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6747 (ttp) REVERT: E 334 TYR cc_start: 0.6962 (OUTLIER) cc_final: 0.6393 (m-10) REVERT: I 13 MET cc_start: 0.5525 (OUTLIER) cc_final: 0.5251 (pp-130) REVERT: J 46 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7522 (pt0) REVERT: J 82 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.8264 (tt0) REVERT: K 13 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6916 (mttm) REVERT: K 46 GLU cc_start: 0.7389 (mt-10) cc_final: 0.7107 (mt-10) REVERT: K 77 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7651 (t0) REVERT: K 110 GLN cc_start: 0.8178 (pt0) cc_final: 0.7931 (pm20) outliers start: 119 outliers final: 64 residues processed: 400 average time/residue: 1.0941 time to fit residues: 496.5170 Evaluate side-chains 409 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 335 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 123 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 206 SER Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 267 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 334 TYR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 13 LYS Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 77 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 1.9990 chunk 113 optimal weight: 0.0870 chunk 2 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 82 optimal weight: 0.4980 chunk 170 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 179 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN C 303 ASN D 88 ASN D 314 GLN E 99 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17849 Z= 0.158 Angle : 0.544 8.577 24284 Z= 0.271 Chirality : 0.042 0.196 2814 Planarity : 0.004 0.052 2985 Dihedral : 5.907 55.973 2888 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.67 % Allowed : 21.03 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.18), residues: 2103 helix: 1.01 (0.21), residues: 568 sheet: -0.52 (0.19), residues: 615 loop : -1.01 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 237 HIS 0.002 0.000 HIS E 318 PHE 0.020 0.001 PHE C 306 TYR 0.033 0.001 TYR E 314 ARG 0.005 0.000 ARG J 102 *********************** 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 432 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 344 time to evaluate : 1.857 Fit side-chains revert: symmetry clash REVERT: A 49 MET cc_start: 0.7190 (ptp) cc_final: 0.6450 (pp-130) REVERT: A 224 GLN cc_start: 0.8328 (tp40) cc_final: 0.7995 (tp-100) REVERT: A 303 ASN cc_start: 0.7233 (t0) cc_final: 0.6991 (t0) REVERT: B 138 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7473 (mt-10) REVERT: B 141 MET cc_start: 0.8789 (mtt) cc_final: 0.8509 (mtt) REVERT: B 229 GLN cc_start: 0.7351 (tp-100) cc_final: 0.7080 (tp-100) REVERT: C 21 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7350 (pttt) REVERT: C 43 ASP cc_start: 0.7954 (m-30) cc_final: 0.7597 (m-30) REVERT: C 227 MET cc_start: 0.7263 (mmm) cc_final: 0.6649 (ttt) REVERT: D 27 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7941 (t0) REVERT: D 90 MET cc_start: 0.8700 (tpp) cc_final: 0.8444 (tpt) REVERT: D 123 GLU cc_start: 0.7733 (pt0) cc_final: 0.7322 (pm20) REVERT: D 170 GLU cc_start: 0.7598 (tp30) cc_final: 0.7386 (tp30) REVERT: E 68 ILE cc_start: 0.8962 (mt) cc_final: 0.8676 (mm) REVERT: E 197 ARG cc_start: 0.7705 (mtp180) cc_final: 0.7297 (mtp180) REVERT: E 199 TYR cc_start: 0.7467 (m-80) cc_final: 0.7041 (m-80) REVERT: E 272 THR cc_start: 0.8819 (t) cc_final: 0.8505 (m) REVERT: E 306 PHE cc_start: 0.7226 (m-10) cc_final: 0.7008 (m-80) REVERT: E 331 MET cc_start: 0.7025 (OUTLIER) cc_final: 0.6668 (ttp) REVERT: E 355 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7352 (mp) REVERT: I 13 MET cc_start: 0.5512 (OUTLIER) cc_final: 0.5235 (pp-130) REVERT: I 61 ARG cc_start: 0.8318 (ptt-90) cc_final: 0.8020 (ptt90) REVERT: J 82 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8198 (tt0) REVERT: J 98 ARG cc_start: 0.8362 (ttp80) cc_final: 0.8115 (ttt90) REVERT: K 13 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6873 (mttm) REVERT: K 19 LYS cc_start: 0.8627 (tptt) cc_final: 0.8346 (tttm) REVERT: K 34 MET cc_start: 0.8816 (mmm) cc_final: 0.8589 (tpt) REVERT: K 46 GLU cc_start: 0.7420 (mt-10) cc_final: 0.7176 (mt-10) REVERT: K 110 GLN cc_start: 0.8151 (pt0) cc_final: 0.7872 (pm20) outliers start: 88 outliers final: 47 residues processed: 383 average time/residue: 1.0977 time to fit residues: 475.8786 Evaluate side-chains 379 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 325 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 27 ASP 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 206 SER Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 150 GLU Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 13 LYS Chi-restraints excluded: chain K residue 17 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 3.9990 chunk 180 optimal weight: 0.2980 chunk 39 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 chunk 166 optimal weight: 0.0070 chunk 92 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 GLN A 185 GLN C 265 ASN D 189 ASN D 314 GLN E 182 GLN I 37 GLN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17849 Z= 0.177 Angle : 0.540 8.486 24284 Z= 0.269 Chirality : 0.043 0.204 2814 Planarity : 0.004 0.052 2985 Dihedral : 5.733 56.084 2888 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 5.20 % Allowed : 21.30 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.18), residues: 2103 helix: 1.11 (0.22), residues: 569 sheet: -0.43 (0.19), residues: 614 loop : -0.89 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 237 HIS 0.002 0.000 HIS B 218 PHE 0.022 0.001 PHE A 240 TYR 0.038 0.001 TYR E 314 ARG 0.004 0.000 ARG K 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 329 time to evaluate : 1.973 Fit side-chains revert: symmetry clash REVERT: A 49 MET cc_start: 0.7216 (ptp) cc_final: 0.6458 (pp-130) REVERT: A 275 ILE cc_start: 0.8854 (OUTLIER) cc_final: 0.8590 (pp) REVERT: A 303 ASN cc_start: 0.7189 (t0) cc_final: 0.6963 (t0) REVERT: B 138 GLU cc_start: 0.7763 (mt-10) cc_final: 0.7484 (mt-10) REVERT: B 141 MET cc_start: 0.8811 (mtt) cc_final: 0.8535 (mtt) REVERT: B 229 GLN cc_start: 0.7361 (tp-100) cc_final: 0.7027 (tp-100) REVERT: B 236 MET cc_start: 0.7104 (mmp) cc_final: 0.6564 (mmp) REVERT: C 21 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7352 (pttt) REVERT: C 43 ASP cc_start: 0.7967 (m-30) cc_final: 0.7608 (m-30) REVERT: C 214 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8588 (mt) REVERT: C 227 MET cc_start: 0.7247 (mmm) cc_final: 0.6644 (ttt) REVERT: D 90 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8401 (tpt) REVERT: D 123 GLU cc_start: 0.7745 (pt0) cc_final: 0.7335 (pm20) REVERT: D 170 GLU cc_start: 0.7551 (tp30) cc_final: 0.7340 (tp30) REVERT: D 249 ARG cc_start: 0.7480 (mtm110) cc_final: 0.7234 (mtm110) REVERT: E 68 ILE cc_start: 0.8970 (mt) cc_final: 0.8685 (mm) REVERT: E 197 ARG cc_start: 0.7664 (mtp180) cc_final: 0.7300 (mtp180) REVERT: E 199 TYR cc_start: 0.7492 (m-80) cc_final: 0.7039 (m-80) REVERT: E 232 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.6860 (ptm-80) REVERT: E 272 THR cc_start: 0.8814 (t) cc_final: 0.8510 (m) REVERT: E 331 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6687 (ttp) REVERT: E 355 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7442 (mp) REVERT: I 13 MET cc_start: 0.5534 (OUTLIER) cc_final: 0.5273 (pp-130) REVERT: I 61 ARG cc_start: 0.8207 (ptt-90) cc_final: 0.7979 (ptt90) REVERT: J 82 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8172 (tt0) REVERT: J 98 ARG cc_start: 0.8350 (ttp80) cc_final: 0.8106 (ttt90) REVERT: K 13 LYS cc_start: 0.7350 (OUTLIER) cc_final: 0.6852 (mttm) REVERT: K 19 LYS cc_start: 0.8578 (tptt) cc_final: 0.8281 (tttm) REVERT: K 46 GLU cc_start: 0.7417 (mt-10) cc_final: 0.7072 (mt-10) REVERT: K 110 GLN cc_start: 0.8178 (pt0) cc_final: 0.7877 (pm20) outliers start: 98 outliers final: 55 residues processed: 372 average time/residue: 1.1481 time to fit residues: 485.9025 Evaluate side-chains 385 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 320 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 55 ASP Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 90 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 13 LYS Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 3.9990 chunk 22 optimal weight: 7.9990 chunk 114 optimal weight: 3.9990 chunk 146 optimal weight: 0.0030 chunk 113 optimal weight: 2.9990 chunk 168 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 199 optimal weight: 5.9990 chunk 124 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 overall best weight: 1.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN D 314 GLN E 99 ASN E 182 GLN I 37 GLN J 5 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.2568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 17849 Z= 0.287 Angle : 0.588 8.828 24284 Z= 0.293 Chirality : 0.045 0.215 2814 Planarity : 0.004 0.051 2985 Dihedral : 5.866 57.169 2888 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 5.10 % Allowed : 21.88 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.18), residues: 2103 helix: 1.11 (0.22), residues: 568 sheet: -0.45 (0.19), residues: 615 loop : -0.82 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 237 HIS 0.003 0.001 HIS D 110 PHE 0.020 0.002 PHE A 240 TYR 0.039 0.002 TYR E 314 ARG 0.007 0.000 ARG A 68 *********************** 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 427 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 331 time to evaluate : 2.059 Fit side-chains revert: symmetry clash REVERT: A 49 MET cc_start: 0.7261 (ptp) cc_final: 0.6510 (pp-130) REVERT: A 125 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8249 (mp) REVERT: A 275 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8618 (pp) REVERT: B 81 MET cc_start: 0.7322 (OUTLIER) cc_final: 0.6867 (ttt) REVERT: B 138 GLU cc_start: 0.7711 (mt-10) cc_final: 0.7486 (mt-10) REVERT: B 141 MET cc_start: 0.8857 (mtt) cc_final: 0.8633 (mtt) REVERT: B 229 GLN cc_start: 0.7381 (tp-100) cc_final: 0.7033 (tp-100) REVERT: C 21 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7380 (pttt) REVERT: C 43 ASP cc_start: 0.8037 (m-30) cc_final: 0.7665 (m-30) REVERT: C 214 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8577 (mt) REVERT: C 227 MET cc_start: 0.7293 (mmm) cc_final: 0.6666 (ttt) REVERT: D 57 ASP cc_start: 0.8416 (m-30) cc_final: 0.8134 (m-30) REVERT: D 90 MET cc_start: 0.8661 (tpp) cc_final: 0.8430 (tpt) REVERT: D 123 GLU cc_start: 0.7811 (pt0) cc_final: 0.7362 (pm20) REVERT: D 170 GLU cc_start: 0.7616 (tp30) cc_final: 0.7398 (tp30) REVERT: D 249 ARG cc_start: 0.7501 (mtm110) cc_final: 0.7268 (mtm110) REVERT: E 68 ILE cc_start: 0.9015 (mt) cc_final: 0.8727 (mm) REVERT: E 150 GLU cc_start: 0.7733 (pp20) cc_final: 0.7486 (tt0) REVERT: E 197 ARG cc_start: 0.7742 (mtp180) cc_final: 0.7410 (mtp180) REVERT: E 199 TYR cc_start: 0.7469 (m-80) cc_final: 0.7076 (m-80) REVERT: E 232 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.6819 (ptm-80) REVERT: E 239 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: E 272 THR cc_start: 0.8850 (t) cc_final: 0.8560 (m) REVERT: E 331 MET cc_start: 0.7008 (OUTLIER) cc_final: 0.6635 (ttp) REVERT: E 333 SER cc_start: 0.8485 (t) cc_final: 0.8207 (p) REVERT: E 336 ARG cc_start: 0.6784 (mtt90) cc_final: 0.6227 (ttm-80) REVERT: E 355 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7421 (mp) REVERT: I 13 MET cc_start: 0.5683 (OUTLIER) cc_final: 0.5411 (pp-130) REVERT: I 61 ARG cc_start: 0.8198 (ptt-90) cc_final: 0.7983 (ptt90) REVERT: J 46 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7482 (pt0) REVERT: J 82 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8186 (tt0) REVERT: J 98 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8123 (ttt90) REVERT: K 19 LYS cc_start: 0.8592 (tptt) cc_final: 0.8286 (tttm) REVERT: K 46 GLU cc_start: 0.7428 (mt-10) cc_final: 0.7042 (mt-10) REVERT: K 110 GLN cc_start: 0.8223 (pt0) cc_final: 0.7888 (pm20) outliers start: 96 outliers final: 62 residues processed: 379 average time/residue: 1.1519 time to fit residues: 492.0224 Evaluate side-chains 395 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 321 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 81 MET Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 222 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 239 ILE Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 93 ILE Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 239 GLN Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 135 optimal weight: 0.0270 chunk 98 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 88 ASN C 265 ASN D 314 GLN E 99 ASN I 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17849 Z= 0.167 Angle : 0.545 8.455 24284 Z= 0.272 Chirality : 0.043 0.198 2814 Planarity : 0.004 0.053 2985 Dihedral : 5.554 56.128 2888 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.46 % Allowed : 22.73 % Favored : 72.81 % 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: -0.14 (0.18), residues: 2103 helix: 1.27 (0.22), residues: 570 sheet: -0.32 (0.20), residues: 598 loop : -0.72 (0.20), residues: 935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 319 HIS 0.002 0.000 HIS D 218 PHE 0.022 0.001 PHE A 240 TYR 0.041 0.001 TYR E 314 ARG 0.007 0.000 ARG A 68 *********************** 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 423 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 339 time to evaluate : 1.986 Fit side-chains revert: symmetry clash REVERT: A 49 MET cc_start: 0.7189 (ptp) cc_final: 0.6425 (pp-130) REVERT: A 242 ILE cc_start: 0.8107 (mm) cc_final: 0.7861 (mm) REVERT: B 138 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7460 (mt-10) REVERT: B 141 MET cc_start: 0.8855 (mtt) cc_final: 0.8533 (mtt) REVERT: B 209 GLU cc_start: 0.7538 (mt-10) cc_final: 0.7291 (mt-10) REVERT: C 43 ASP cc_start: 0.7999 (m-30) cc_final: 0.7617 (m-30) REVERT: C 214 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8579 (mt) REVERT: C 227 MET cc_start: 0.7253 (mmm) cc_final: 0.6626 (ttt) REVERT: D 57 ASP cc_start: 0.8375 (m-30) cc_final: 0.8113 (m-30) REVERT: D 90 MET cc_start: 0.8622 (tpp) cc_final: 0.8393 (tpt) REVERT: D 123 GLU cc_start: 0.7773 (pt0) cc_final: 0.7311 (pm20) REVERT: D 170 GLU cc_start: 0.7579 (tp30) cc_final: 0.7337 (tp30) REVERT: D 249 ARG cc_start: 0.7486 (mtm110) cc_final: 0.7268 (mtm110) REVERT: D 271 ILE cc_start: 0.8727 (mp) cc_final: 0.8377 (mp) REVERT: E 68 ILE cc_start: 0.8983 (mt) cc_final: 0.8683 (mm) REVERT: E 197 ARG cc_start: 0.7589 (mtp180) cc_final: 0.7293 (mtp180) REVERT: E 199 TYR cc_start: 0.7475 (m-80) cc_final: 0.7080 (m-80) REVERT: E 232 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.6787 (ptm-80) REVERT: E 331 MET cc_start: 0.7044 (OUTLIER) cc_final: 0.6660 (ttp) REVERT: E 333 SER cc_start: 0.8464 (t) cc_final: 0.8201 (p) REVERT: E 336 ARG cc_start: 0.6728 (mtt90) cc_final: 0.6400 (ttm110) REVERT: I 13 MET cc_start: 0.5587 (OUTLIER) cc_final: 0.5318 (pp-130) REVERT: J 82 GLN cc_start: 0.8723 (OUTLIER) cc_final: 0.8182 (tt0) REVERT: J 98 ARG cc_start: 0.8346 (ttp80) cc_final: 0.8126 (ttt90) REVERT: K 19 LYS cc_start: 0.8530 (tptt) cc_final: 0.8215 (tttm) REVERT: K 46 GLU cc_start: 0.7400 (mt-10) cc_final: 0.7068 (mt-10) REVERT: K 110 GLN cc_start: 0.8205 (pt0) cc_final: 0.7896 (pm20) outliers start: 84 outliers final: 58 residues processed: 379 average time/residue: 1.1342 time to fit residues: 485.2484 Evaluate side-chains 384 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 321 time to evaluate : 1.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ASP Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 203 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 228 ILE Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 172 ASP Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 5.9990 chunk 191 optimal weight: 0.0980 chunk 174 optimal weight: 2.9990 chunk 185 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 168 optimal weight: 0.9990 chunk 175 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN D 314 GLN E 182 GLN I 37 GLN J 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17849 Z= 0.204 Angle : 0.556 8.924 24284 Z= 0.276 Chirality : 0.043 0.208 2814 Planarity : 0.004 0.052 2985 Dihedral : 5.457 55.813 2884 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.98 % Allowed : 23.31 % Favored : 72.70 % 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: -0.10 (0.18), residues: 2103 helix: 1.32 (0.22), residues: 570 sheet: -0.36 (0.20), residues: 610 loop : -0.64 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 237 HIS 0.002 0.000 HIS D 218 PHE 0.026 0.001 PHE A 240 TYR 0.043 0.001 TYR E 314 ARG 0.008 0.000 ARG L 54 *********************** 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 406 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 331 time to evaluate : 2.072 Fit side-chains revert: symmetry clash REVERT: A 49 MET cc_start: 0.7194 (ptp) cc_final: 0.6430 (pp-130) REVERT: A 242 ILE cc_start: 0.8099 (mm) cc_final: 0.7846 (mm) REVERT: B 138 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7485 (mt-10) REVERT: B 141 MET cc_start: 0.8864 (mtt) cc_final: 0.8597 (mtt) REVERT: B 209 GLU cc_start: 0.7589 (mt-10) cc_final: 0.7332 (mt-10) REVERT: C 21 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7299 (pttt) REVERT: C 43 ASP cc_start: 0.8007 (m-30) cc_final: 0.7648 (m-30) REVERT: C 214 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8574 (mt) REVERT: C 227 MET cc_start: 0.7263 (mmm) cc_final: 0.6632 (ttt) REVERT: D 57 ASP cc_start: 0.8389 (m-30) cc_final: 0.8127 (m-30) REVERT: D 123 GLU cc_start: 0.7752 (pt0) cc_final: 0.7286 (pm20) REVERT: D 170 GLU cc_start: 0.7597 (tp30) cc_final: 0.7346 (tp30) REVERT: E 68 ILE cc_start: 0.8987 (mt) cc_final: 0.8687 (mm) REVERT: E 197 ARG cc_start: 0.7614 (mtp180) cc_final: 0.7298 (mtp180) REVERT: E 199 TYR cc_start: 0.7447 (m-80) cc_final: 0.7036 (m-80) REVERT: E 232 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.6845 (ptm-80) REVERT: E 239 GLN cc_start: 0.8086 (OUTLIER) cc_final: 0.7677 (tt0) REVERT: E 272 THR cc_start: 0.8889 (t) cc_final: 0.8570 (m) REVERT: E 331 MET cc_start: 0.6976 (OUTLIER) cc_final: 0.6600 (ttp) REVERT: E 333 SER cc_start: 0.8471 (t) cc_final: 0.8205 (p) REVERT: E 336 ARG cc_start: 0.6739 (mtt90) cc_final: 0.6412 (ttm110) REVERT: I 13 MET cc_start: 0.5610 (OUTLIER) cc_final: 0.5352 (pp-130) REVERT: J 46 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7460 (pt0) REVERT: J 82 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8185 (tt0) REVERT: J 98 ARG cc_start: 0.8350 (ttp80) cc_final: 0.8127 (ttt90) REVERT: K 34 MET cc_start: 0.8782 (mmm) cc_final: 0.8511 (tpt) REVERT: K 46 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7075 (mt-10) outliers start: 75 outliers final: 56 residues processed: 367 average time/residue: 1.1849 time to fit residues: 489.3263 Evaluate side-chains 386 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 322 time to evaluate : 1.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 36 GLU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 206 SER Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 99 ASN Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 239 GLN Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain I residue 10 SER Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 46 GLU Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 206 optimal weight: 0.7980 chunk 189 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 100 optimal weight: 0.0060 chunk 130 optimal weight: 4.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN C 265 ASN D 314 GLN I 37 GLN J 5 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 17849 Z= 0.168 Angle : 0.546 9.736 24284 Z= 0.271 Chirality : 0.042 0.200 2814 Planarity : 0.004 0.052 2985 Dihedral : 5.318 55.278 2884 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.72 % Allowed : 24.11 % Favored : 72.17 % 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: -0.03 (0.18), residues: 2103 helix: 1.38 (0.22), residues: 570 sheet: -0.33 (0.20), residues: 610 loop : -0.60 (0.21), residues: 923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 237 HIS 0.002 0.000 HIS D 218 PHE 0.026 0.001 PHE A 240 TYR 0.043 0.001 TYR E 314 ARG 0.009 0.000 ARG L 54 ********************** 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 401 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 331 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 MET cc_start: 0.7204 (ptp) cc_final: 0.6476 (pp-130) REVERT: A 242 ILE cc_start: 0.8062 (mm) cc_final: 0.7788 (mm) REVERT: A 275 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8585 (pp) REVERT: B 138 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7491 (mt-10) REVERT: B 141 MET cc_start: 0.8870 (mtt) cc_final: 0.8569 (mtt) REVERT: C 21 LYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7265 (pttt) REVERT: C 43 ASP cc_start: 0.7997 (m-30) cc_final: 0.7628 (m-30) REVERT: C 214 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8551 (mt) REVERT: C 227 MET cc_start: 0.7234 (mmm) cc_final: 0.6595 (ttt) REVERT: C 303 ASN cc_start: 0.7619 (t0) cc_final: 0.7369 (t0) REVERT: D 57 ASP cc_start: 0.8346 (m-30) cc_final: 0.8126 (m-30) REVERT: D 123 GLU cc_start: 0.7766 (pt0) cc_final: 0.7271 (pm20) REVERT: D 170 GLU cc_start: 0.7577 (tp30) cc_final: 0.7343 (tp30) REVERT: D 271 ILE cc_start: 0.8670 (mp) cc_final: 0.8328 (mp) REVERT: E 68 ILE cc_start: 0.8969 (mt) cc_final: 0.8663 (mm) REVERT: E 197 ARG cc_start: 0.7602 (mtp180) cc_final: 0.7302 (mtp180) REVERT: E 199 TYR cc_start: 0.7469 (m-80) cc_final: 0.7063 (m-80) REVERT: E 232 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.6911 (ptm-80) REVERT: E 272 THR cc_start: 0.8877 (t) cc_final: 0.8555 (m) REVERT: E 331 MET cc_start: 0.6998 (OUTLIER) cc_final: 0.6612 (ttp) REVERT: E 333 SER cc_start: 0.8468 (t) cc_final: 0.8202 (p) REVERT: E 336 ARG cc_start: 0.6688 (mtt90) cc_final: 0.6409 (ttm110) REVERT: I 13 MET cc_start: 0.5730 (OUTLIER) cc_final: 0.5491 (pp-130) REVERT: J 82 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: J 98 ARG cc_start: 0.8336 (ttp80) cc_final: 0.8125 (ttt90) REVERT: K 19 LYS cc_start: 0.8500 (tptt) cc_final: 0.8242 (tptm) REVERT: K 34 MET cc_start: 0.8758 (mmm) cc_final: 0.8520 (tpt) REVERT: K 46 GLU cc_start: 0.7401 (mt-10) cc_final: 0.7079 (mt-10) REVERT: K 59 LYS cc_start: 0.8521 (mptt) cc_final: 0.8235 (mmtm) outliers start: 70 outliers final: 52 residues processed: 363 average time/residue: 1.1573 time to fit residues: 473.3139 Evaluate side-chains 386 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 327 time to evaluate : 1.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 222 ILE Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 255 ILE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 21 ARG Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 21 LYS Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 49 MET Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 75 ASN Chi-restraints excluded: chain C residue 201 SER Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain C residue 275 ILE Chi-restraints excluded: chain C residue 294 MET Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 314 GLN Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 189 GLU Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 232 ARG Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 287 LEU Chi-restraints excluded: chain E residue 331 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 18 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 82 GLN Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.0670 chunk 50 optimal weight: 0.6980 chunk 151 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 68 optimal weight: 0.0980 chunk 168 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** B 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 ASN D 314 GLN E 99 ASN E 182 GLN I 37 GLN J 5 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.145272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.103800 restraints weight = 21682.204| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.05 r_work: 0.3156 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17849 Z= 0.194 Angle : 0.554 9.298 24284 Z= 0.274 Chirality : 0.043 0.204 2814 Planarity : 0.004 0.051 2985 Dihedral : 5.324 55.236 2884 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.72 % Allowed : 23.90 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.18), residues: 2103 helix: 1.40 (0.22), residues: 570 sheet: -0.27 (0.20), residues: 620 loop : -0.57 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 237 HIS 0.002 0.000 HIS D 218 PHE 0.025 0.001 PHE E 338 TYR 0.043 0.001 TYR E 314 ARG 0.008 0.000 ARG L 54 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7765.77 seconds wall clock time: 137 minutes 36.37 seconds (8256.37 seconds total)