Starting phenix.real_space_refine on Sat Feb 17 03:41:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3z_22037/02_2024/6x3z_22037_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3z_22037/02_2024/6x3z_22037.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3z_22037/02_2024/6x3z_22037.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3z_22037/02_2024/6x3z_22037.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3z_22037/02_2024/6x3z_22037_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3z_22037/02_2024/6x3z_22037_updated.pdb" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 11211 2.51 5 N 2828 2.21 5 O 3229 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C ARG 318": "NH1" <-> "NH2" Residue "C ARG 321": "NH1" <-> "NH2" Residue "D ARG 17": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D ARG 173": "NH1" <-> "NH2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E ASP 148": "OD1" <-> "OD2" 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 313": "OE1" <-> "OE2" Residue "E ARG 327": "NH1" <-> "NH2" Residue "E TYR 350": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I GLU 104": "OE1" <-> "OE2" Residue "J GLU 42": "OE1" <-> "OE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "J ARG 102": "NH1" <-> "NH2" Residue "L GLU 27": "OE1" <-> "OE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "K GLU 10": "OE1" <-> "OE2" Residue "K TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 42": "OE1" <-> "OE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K ARG 98": "NH1" <-> "NH2" Residue "K ARG 102": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17365 Number of models: 1 Model: "" Number of chains: 16 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: 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: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 9.88, per 1000 atoms: 0.57 Number of scatterers: 17365 At special positions: 0 Unit cell: (134.475, 146.025, 106.425, 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 3229 8.00 N 2828 7.00 C 11211 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=2.02 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=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.04 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-ASN " NAG A 404 " - " ASN A 80 " " NAG C 404 " - " ASN C 80 " " NAG D 401 " - " ASN D 111 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN E 208 " Time building additional restraints: 7.03 Conformation dependent library (CDL) restraints added in 3.1 seconds 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4020 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 27 sheets defined 27.9% alpha, 29.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.25 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.569A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) 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: 4.121A pdb=" N LEU A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N MET A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix removed outlier: 4.976A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.729A 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: 3.522A 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 229 removed outlier: 4.032A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 246 removed outlier: 4.192A pdb=" N SER B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N PHE B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TRP B 246 " --> pdb=" O GLN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 273 Processing helix chain 'B' and resid 285 through 310 Processing helix chain 'B' and resid 315 through 344 removed outlier: 4.143A pdb=" N ALA B 319 " --> pdb=" O PRO B 315 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix Processing helix chain 'C' and resid 9 through 19 Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 219 through 241 removed outlier: 5.042A pdb=" N MET C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix removed outlier: 3.735A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 269 Processing helix chain 'C' and resid 280 through 304 Processing helix chain 'C' and resid 310 through 338 removed outlier: 3.569A 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 229 removed outlier: 3.789A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 246 removed outlier: 4.144A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.690A 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: 3.846A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N PHE D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Proline residue: D 330 - end of helix Processing helix chain 'E' and resid 26 through 34 Processing helix chain 'E' and resid 100 through 105 removed outlier: 4.429A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 255 removed outlier: 5.595A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix removed outlier: 3.564A pdb=" N VAL E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER E 254 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N PHE E 255 " --> pdb=" O SER E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 286 removed outlier: 3.691A pdb=" N LYS E 285 " --> pdb=" O THR E 281 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N SER E 286 " --> pdb=" O ILE E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 323 removed outlier: 4.313A 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 328 No H-bonds generated for 'chain 'E' and resid 325 through 328' Processing helix chain 'E' and resid 330 through 356 removed outlier: 3.953A 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: 6.276A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.523A 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: 3.752A pdb=" N CYS A 150 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N PHE A 212 " --> pdb=" O CYS A 150 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.747A 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: 6.877A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.813A 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: 6.186A pdb=" N THR B 39 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N GLU B 170 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N VAL B 41 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 4.176A 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: 4.075A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.595A 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: 6.440A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 3.749A 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: 3.638A pdb=" N CYS C 150 " --> pdb=" O PHE C 212 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N PHE C 212 " --> pdb=" O CYS C 150 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.560A 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: 6.847A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 7.064A 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: 6.344A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 45 through 47 Processing sheet with id= L, first strand: chain 'D' and resid 99 through 101 removed outlier: 3.804A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 179 through 183 removed outlier: 5.777A pdb=" N THR E 51 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N GLN E 182 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE E 53 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 188 through 190 removed outlier: 6.535A pdb=" N MET E 57 " --> pdb=" O GLU E 189 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.678A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 116 through 121 removed outlier: 7.084A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 4 through 7 Processing sheet with id= R, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.310A pdb=" N LYS I 102 " --> pdb=" O MET I 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'I' and resid 85 through 90 removed outlier: 6.289A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 3 through 6 Processing sheet with id= U, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.505A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N LYS J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N TRP J 47 " --> pdb=" O LYS J 38 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= W, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.064A pdb=" N LYS L 102 " --> pdb=" O MET L 11 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N MET L 13 " --> pdb=" O LYS L 102 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N GLU L 104 " --> pdb=" O MET L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'L' and resid 85 through 90 removed outlier: 6.114A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.253A 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: 6.905A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N TYR K 33 " --> pdb=" O LYS K 99 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 730 hydrogen bonds defined for protein. 2133 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: 5.32 Time building geometry restraints manager: 7.55 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: 4287 1.33 - 1.46: 4733 1.46 - 1.58: 8612 1.58 - 1.71: 0 1.71 - 1.83: 167 Bond restraints: 17799 Sorted by residual: bond pdb=" CD ABU A 405 " pdb=" OE1 ABU A 405 " ideal model delta sigma weight residual 1.247 1.336 -0.089 2.00e-02 2.50e+03 1.98e+01 bond pdb=" CD ABU C 405 " pdb=" OE2 ABU C 405 " ideal model delta sigma weight residual 1.250 1.338 -0.088 2.00e-02 2.50e+03 1.92e+01 bond pdb=" N GLN A 148 " pdb=" CA GLN A 148 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.21e-02 6.83e+03 7.78e+00 bond pdb=" N ASN E 208 " pdb=" CA ASN E 208 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.15e-02 7.56e+03 7.64e+00 bond pdb=" N SER C 211 " pdb=" CA SER C 211 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.23e-02 6.61e+03 7.15e+00 ... (remaining 17794 not shown) Histogram of bond angle deviations from ideal: 96.93 - 104.74: 322 104.74 - 112.55: 9053 112.55 - 120.36: 7537 120.36 - 128.18: 7119 128.18 - 135.99: 173 Bond angle restraints: 24204 Sorted by residual: angle pdb=" CA ARG C 269 " pdb=" CB ARG C 269 " pdb=" CG ARG C 269 " ideal model delta sigma weight residual 114.10 126.39 -12.29 2.00e+00 2.50e-01 3.77e+01 angle pdb=" CA LEU E 345 " pdb=" CB LEU E 345 " pdb=" CG LEU E 345 " ideal model delta sigma weight residual 116.30 135.99 -19.69 3.50e+00 8.16e-02 3.16e+01 angle pdb=" CA THR I 31 " pdb=" CB THR I 31 " pdb=" CG2 THR I 31 " ideal model delta sigma weight residual 110.50 118.08 -7.58 1.70e+00 3.46e-01 1.99e+01 angle pdb=" C CYS C 150 " pdb=" CA CYS C 150 " pdb=" CB CYS C 150 " ideal model delta sigma weight residual 109.35 117.96 -8.61 1.98e+00 2.55e-01 1.89e+01 angle pdb=" C CYS A 150 " pdb=" CA CYS A 150 " pdb=" CB CYS A 150 " ideal model delta sigma weight residual 109.70 117.49 -7.79 1.81e+00 3.05e-01 1.85e+01 ... (remaining 24199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.85: 10079 21.85 - 43.71: 592 43.71 - 65.56: 46 65.56 - 87.41: 37 87.41 - 109.26: 14 Dihedral angle restraints: 10768 sinusoidal: 4512 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 -7.40 -78.60 1 1.00e+01 1.00e-02 7.70e+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 -13.57 -72.43 1 1.00e+01 1.00e-02 6.70e+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 -19.82 -66.18 1 1.00e+01 1.00e-02 5.72e+01 ... (remaining 10765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.914: 2795 0.914 - 1.827: 0 1.827 - 2.741: 0 2.741 - 3.655: 0 3.655 - 4.569: 2 Chirality restraints: 2797 Sorted by residual: chirality pdb=" C1 MAN G 9 " pdb=" O2 MAN G 8 " pdb=" C2 MAN G 9 " pdb=" O5 MAN G 9 " both_signs ideal model delta sigma weight residual False 2.40 1.63 0.77 2.00e-02 2.50e+03 1.47e+03 chirality pdb=" C1 MAN G 6 " pdb=" O2 MAN G 5 " pdb=" C2 MAN G 6 " pdb=" O5 MAN G 6 " both_signs ideal model delta sigma weight residual False 2.40 1.66 0.74 2.00e-02 2.50e+03 1.37e+03 chirality pdb=" C1 MAN G 4 " pdb=" O3 BMA G 3 " pdb=" C2 MAN G 4 " pdb=" O5 MAN G 4 " both_signs ideal model delta sigma weight residual False 2.40 1.70 0.70 2.00e-02 2.50e+03 1.22e+03 ... (remaining 2794 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.289 2.00e-02 2.50e+03 2.43e-01 7.36e+02 pdb=" C7 NAG M 2 " 0.075 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.185 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.414 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " 0.150 2.00e-02 2.50e+03 1.26e-01 1.99e+02 pdb=" C7 NAG M 1 " -0.030 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " -0.036 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " -0.202 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " 0.119 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " 0.146 2.00e-02 2.50e+03 1.20e-01 1.81e+02 pdb=" C7 NAG F 2 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " 0.108 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " -0.195 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.020 2.00e-02 2.50e+03 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2930 2.77 - 3.30: 15424 3.30 - 3.83: 29582 3.83 - 4.37: 35297 4.37 - 4.90: 62045 Nonbonded interactions: 145278 Sorted by model distance: nonbonded pdb=" O VAL B 257 " pdb=" OG1 THR B 261 " model vdw 2.232 2.440 nonbonded pdb=" OH TYR C 226 " pdb=" OH TYR C 335 " model vdw 2.283 2.440 nonbonded pdb=" OG1 THR B 99 " pdb=" OH TYR B 169 " model vdw 2.286 2.440 nonbonded pdb=" O THR C 256 " pdb=" OG1 THR C 260 " model vdw 2.287 2.440 nonbonded pdb=" OG1 THR E 111 " pdb=" OH TYR E 181 " model vdw 2.308 2.440 ... (remaining 145273 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' } 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: 12.640 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: 0.000 Extract box with map and model: 2.950 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 47.700 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 0.007 0.089 17799 Z= 0.469 Angle : 1.089 19.690 24204 Z= 0.573 Chirality : 0.142 4.569 2797 Planarity : 0.009 0.243 2981 Dihedral : 14.388 109.265 6721 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.69 % Allowed : 5.63 % Favored : 93.68 % Cbeta Deviations : 0.10 % 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: -2.07 (0.16), residues: 2103 helix: -0.27 (0.20), residues: 564 sheet: -0.96 (0.19), residues: 632 loop : -2.37 (0.17), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 336 HIS 0.005 0.002 HIS B 151 PHE 0.045 0.004 PHE B 258 TYR 0.042 0.003 TYR C 157 ARG 0.010 0.001 ARG C 269 *********************** 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 422 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 409 time to evaluate : 1.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 LEU cc_start: 0.8493 (mt) cc_final: 0.8217 (mp) REVERT: A 319 TRP cc_start: 0.7432 (t60) cc_final: 0.6880 (t-100) REVERT: B 24 ASP cc_start: 0.7732 (t0) cc_final: 0.7253 (p0) REVERT: B 71 LYS cc_start: 0.8337 (tttp) cc_final: 0.8092 (tttp) REVERT: B 73 GLU cc_start: 0.8052 (mm-30) cc_final: 0.7826 (mm-30) REVERT: B 98 ASP cc_start: 0.7600 (p0) cc_final: 0.7227 (p0) REVERT: B 335 ILE cc_start: 0.8155 (pt) cc_final: 0.7906 (mp) REVERT: C 41 ASN cc_start: 0.7848 (m110) cc_final: 0.7347 (t0) REVERT: C 54 ASN cc_start: 0.8106 (m110) cc_final: 0.7851 (m110) REVERT: C 137 MET cc_start: 0.8279 (mmm) cc_final: 0.7985 (mmm) REVERT: D 93 LYS cc_start: 0.7971 (mmmt) cc_final: 0.7734 (tptp) REVERT: E 33 ASN cc_start: 0.8174 (m-40) cc_final: 0.7907 (m-40) REVERT: I 13 MET cc_start: 0.7054 (ppp) cc_final: 0.6479 (ppp) REVERT: I 60 ASP cc_start: 0.8418 (t70) cc_final: 0.8206 (t0) REVERT: J 46 GLU cc_start: 0.8170 (tt0) cc_final: 0.7871 (tt0) REVERT: J 63 LYS cc_start: 0.8741 (mttp) cc_final: 0.8529 (ttpt) REVERT: J 65 GLN cc_start: 0.8115 (tp40) cc_final: 0.7882 (tp40) REVERT: J 80 TYR cc_start: 0.8792 (m-80) cc_final: 0.8368 (m-80) REVERT: K 73 ASP cc_start: 0.8170 (t0) cc_final: 0.7765 (t0) outliers start: 13 outliers final: 3 residues processed: 417 average time/residue: 0.3170 time to fit residues: 192.1378 Evaluate side-chains 323 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 320 time to evaluate : 2.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 211 SER Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain L residue 79 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 120 optimal weight: 3.9990 chunk 187 optimal weight: 20.0000 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 54 ASN A 65 GLN A 185 GLN A 332 ASN B 68 GLN B 242 GLN C 65 GLN C 303 ASN C 309 GLN D 68 GLN D 102 HIS D 189 ASN D 275 ASN D 308 ASN D 314 GLN D 346 ASN E 128 ASN E 239 GLN I 38 GLN J 6 GLN K 6 GLN K 110 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17799 Z= 0.202 Angle : 0.613 12.051 24204 Z= 0.300 Chirality : 0.050 0.951 2797 Planarity : 0.004 0.043 2981 Dihedral : 8.470 76.613 2787 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.59 % Allowed : 11.90 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.17), residues: 2103 helix: 0.53 (0.21), residues: 558 sheet: -0.86 (0.19), residues: 650 loop : -1.84 (0.19), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 252 HIS 0.003 0.001 HIS D 216 PHE 0.026 0.002 PHE E 346 TYR 0.017 0.001 TYR E 314 ARG 0.007 0.000 ARG E 197 *********************** 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 363 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 333 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 304 TYR cc_start: 0.6946 (t80) cc_final: 0.6740 (t80) REVERT: A 319 TRP cc_start: 0.7453 (t60) cc_final: 0.6922 (t-100) REVERT: B 24 ASP cc_start: 0.7673 (t0) cc_final: 0.7220 (p0) REVERT: B 71 LYS cc_start: 0.8208 (tttp) cc_final: 0.7927 (tptm) REVERT: B 98 ASP cc_start: 0.7580 (p0) cc_final: 0.7234 (p0) REVERT: C 41 ASN cc_start: 0.8002 (m110) cc_final: 0.7483 (t0) REVERT: C 49 MET cc_start: 0.7339 (ptp) cc_final: 0.6989 (ptp) REVERT: C 54 ASN cc_start: 0.8152 (m110) cc_final: 0.7896 (m110) REVERT: C 68 ARG cc_start: 0.8210 (ttt-90) cc_final: 0.7988 (ttt-90) REVERT: C 323 PHE cc_start: 0.5874 (m-10) cc_final: 0.5617 (m-10) REVERT: D 58 MET cc_start: 0.8379 (mmm) cc_final: 0.7840 (mtm) REVERT: D 93 LYS cc_start: 0.8078 (mmmt) cc_final: 0.7858 (tptp) REVERT: D 112 MET cc_start: 0.8056 (tpp) cc_final: 0.7258 (tpp) REVERT: E 33 ASN cc_start: 0.8153 (m-40) cc_final: 0.7913 (m-40) REVERT: I 13 MET cc_start: 0.7145 (ppp) cc_final: 0.6533 (ppp) REVERT: I 60 ASP cc_start: 0.8413 (t70) cc_final: 0.8150 (t0) REVERT: J 46 GLU cc_start: 0.8201 (tt0) cc_final: 0.7898 (tt0) REVERT: J 65 GLN cc_start: 0.8105 (tp40) cc_final: 0.7860 (tp40) REVERT: J 80 TYR cc_start: 0.8949 (m-80) cc_final: 0.8591 (m-80) REVERT: K 73 ASP cc_start: 0.8108 (t0) cc_final: 0.7663 (t0) outliers start: 30 outliers final: 21 residues processed: 347 average time/residue: 0.3015 time to fit residues: 155.8984 Evaluate side-chains 321 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 300 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 244 TYR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 138 MET Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 239 GLN Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain J residue 37 VAL Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 0.6980 chunk 58 optimal weight: 9.9990 chunk 156 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 51 optimal weight: 0.6980 chunk 188 optimal weight: 2.9990 chunk 203 optimal weight: 9.9990 chunk 167 optimal weight: 0.7980 chunk 186 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 116 ASN D 116 ASN D 337 ASN I 1 ASN L 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17799 Z= 0.298 Angle : 0.612 10.628 24204 Z= 0.301 Chirality : 0.044 0.318 2797 Planarity : 0.004 0.044 2981 Dihedral : 6.997 65.902 2783 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.44 % Allowed : 14.02 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.17), residues: 2103 helix: 0.76 (0.21), residues: 564 sheet: -0.81 (0.19), residues: 628 loop : -1.55 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 252 HIS 0.004 0.001 HIS D 110 PHE 0.023 0.002 PHE E 304 TYR 0.021 0.001 TYR B 294 ARG 0.008 0.000 ARG I 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 323 time to evaluate : 2.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8395 (mtm110) cc_final: 0.8157 (mtm180) REVERT: A 227 MET cc_start: 0.7154 (ttp) cc_final: 0.6278 (ttp) REVERT: A 319 TRP cc_start: 0.7463 (t60) cc_final: 0.6856 (t-100) REVERT: B 24 ASP cc_start: 0.7726 (t0) cc_final: 0.7321 (p0) REVERT: B 58 MET cc_start: 0.8395 (mmm) cc_final: 0.8157 (mmm) REVERT: B 294 TYR cc_start: 0.7006 (t80) cc_final: 0.6733 (t80) REVERT: B 335 ILE cc_start: 0.8180 (pt) cc_final: 0.7974 (mp) REVERT: C 9 MET cc_start: 0.8247 (tpp) cc_final: 0.8024 (tpp) REVERT: C 54 ASN cc_start: 0.8251 (m110) cc_final: 0.8007 (m110) REVERT: C 68 ARG cc_start: 0.8244 (ttt-90) cc_final: 0.8016 (ttt-90) REVERT: C 289 PHE cc_start: 0.7464 (t80) cc_final: 0.6781 (t80) REVERT: D 58 MET cc_start: 0.8413 (mmm) cc_final: 0.7880 (mtm) REVERT: D 93 LYS cc_start: 0.8237 (mmmt) cc_final: 0.7968 (tptp) REVERT: D 112 MET cc_start: 0.8104 (tpp) cc_final: 0.7416 (tpp) REVERT: D 236 MET cc_start: 0.6537 (mtt) cc_final: 0.6165 (mtp) REVERT: E 324 GLN cc_start: 0.6749 (pm20) cc_final: 0.6510 (pm20) REVERT: I 13 MET cc_start: 0.7226 (ppp) cc_final: 0.6735 (ppp) REVERT: I 60 ASP cc_start: 0.8428 (t70) cc_final: 0.8218 (t0) REVERT: J 19 LYS cc_start: 0.9001 (tptt) cc_final: 0.8699 (tptp) REVERT: J 65 GLN cc_start: 0.8127 (tp40) cc_final: 0.7886 (tp40) REVERT: L 63 THR cc_start: 0.8797 (OUTLIER) cc_final: 0.8360 (p) REVERT: K 73 ASP cc_start: 0.8141 (t0) cc_final: 0.7675 (t0) outliers start: 46 outliers final: 32 residues processed: 347 average time/residue: 0.3002 time to fit residues: 156.8544 Evaluate side-chains 340 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 307 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 5.9990 chunk 141 optimal weight: 4.9990 chunk 97 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 200 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN ** D 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS ** E 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 17799 Z= 0.406 Angle : 0.655 10.068 24204 Z= 0.325 Chirality : 0.046 0.336 2797 Planarity : 0.004 0.056 2981 Dihedral : 6.452 54.660 2783 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.66 % Allowed : 15.14 % Favored : 81.20 % 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: -0.89 (0.18), residues: 2103 helix: 1.01 (0.22), residues: 558 sheet: -0.83 (0.19), residues: 633 loop : -1.36 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 252 HIS 0.004 0.001 HIS D 110 PHE 0.032 0.002 PHE E 346 TYR 0.019 0.002 TYR B 294 ARG 0.012 0.001 ARG I 61 *********************** 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 382 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 313 time to evaluate : 2.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8439 (mtm110) cc_final: 0.8181 (mtm180) REVERT: A 319 TRP cc_start: 0.7524 (t60) cc_final: 0.6917 (t-100) REVERT: B 24 ASP cc_start: 0.7845 (t0) cc_final: 0.7455 (p0) REVERT: B 294 TYR cc_start: 0.7102 (t80) cc_final: 0.6876 (t80) REVERT: C 49 MET cc_start: 0.7408 (ptp) cc_final: 0.6966 (ptp) REVERT: C 54 ASN cc_start: 0.8464 (m110) cc_final: 0.8177 (m110) REVERT: C 59 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8453 (pt) REVERT: C 68 ARG cc_start: 0.8262 (ttt-90) cc_final: 0.7977 (ttt-90) REVERT: D 58 MET cc_start: 0.8430 (mmm) cc_final: 0.7758 (mtm) REVERT: D 112 MET cc_start: 0.8172 (tpp) cc_final: 0.7339 (tpp) REVERT: D 133 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8697 (pp) REVERT: E 304 PHE cc_start: 0.8402 (t80) cc_final: 0.8181 (t80) REVERT: E 324 GLN cc_start: 0.6903 (pm20) cc_final: 0.6683 (pm20) REVERT: I 13 MET cc_start: 0.7285 (ppp) cc_final: 0.6895 (ppp) REVERT: I 49 TYR cc_start: 0.8474 (p90) cc_final: 0.8194 (p90) REVERT: J 65 GLN cc_start: 0.8135 (tp40) cc_final: 0.7932 (tp40) REVERT: J 80 TYR cc_start: 0.9102 (m-80) cc_final: 0.8880 (m-80) outliers start: 69 outliers final: 44 residues processed: 352 average time/residue: 0.2885 time to fit residues: 153.5912 Evaluate side-chains 353 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 307 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 21 LEU Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 69 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 170 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 102 optimal weight: 0.9980 chunk 179 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 17799 Z= 0.337 Angle : 0.620 11.053 24204 Z= 0.307 Chirality : 0.045 0.275 2797 Planarity : 0.004 0.051 2981 Dihedral : 6.357 59.352 2783 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.51 % Allowed : 16.62 % Favored : 79.87 % 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: -0.73 (0.18), residues: 2103 helix: 1.04 (0.22), residues: 566 sheet: -0.74 (0.20), residues: 611 loop : -1.20 (0.20), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 252 HIS 0.003 0.001 HIS D 110 PHE 0.020 0.002 PHE E 158 TYR 0.016 0.002 TYR B 294 ARG 0.007 0.000 ARG I 61 *********************** 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 378 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 312 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8440 (mtm110) cc_final: 0.8186 (mtm180) REVERT: A 319 TRP cc_start: 0.7471 (t60) cc_final: 0.6859 (t-100) REVERT: B 24 ASP cc_start: 0.7919 (t0) cc_final: 0.7522 (p0) REVERT: B 71 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8186 (tptm) REVERT: B 294 TYR cc_start: 0.7182 (t80) cc_final: 0.6920 (t80) REVERT: C 54 ASN cc_start: 0.8467 (m110) cc_final: 0.8157 (m-40) REVERT: C 59 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8478 (pt) REVERT: C 68 ARG cc_start: 0.8254 (ttt-90) cc_final: 0.7986 (ttt-90) REVERT: D 112 MET cc_start: 0.8172 (tpp) cc_final: 0.7381 (tpp) REVERT: E 324 GLN cc_start: 0.6970 (pm20) cc_final: 0.6762 (pm20) REVERT: J 65 GLN cc_start: 0.8147 (tp40) cc_final: 0.7939 (tp40) outliers start: 66 outliers final: 49 residues processed: 351 average time/residue: 0.2844 time to fit residues: 151.5796 Evaluate side-chains 358 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 307 time to evaluate : 1.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 71 LYS Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 324 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain E residue 355 LEU Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 63 THR Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 90 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 0.0270 chunk 180 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 117 optimal weight: 0.7980 chunk 49 optimal weight: 0.5980 chunk 200 optimal weight: 6.9990 chunk 166 optimal weight: 20.0000 chunk 92 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17799 Z= 0.170 Angle : 0.563 10.304 24204 Z= 0.279 Chirality : 0.043 0.374 2797 Planarity : 0.004 0.041 2981 Dihedral : 5.960 59.313 2783 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.92 % Allowed : 18.11 % Favored : 78.97 % 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: -0.44 (0.18), residues: 2103 helix: 1.41 (0.22), residues: 551 sheet: -0.61 (0.20), residues: 614 loop : -1.03 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 252 HIS 0.002 0.000 HIS B 102 PHE 0.018 0.001 PHE E 158 TYR 0.014 0.001 TYR C 299 ARG 0.011 0.000 ARG I 61 *********************** 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 375 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 320 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8418 (mtm110) cc_final: 0.8186 (mtm180) REVERT: A 319 TRP cc_start: 0.7349 (t60) cc_final: 0.6770 (t-100) REVERT: B 24 ASP cc_start: 0.7900 (t0) cc_final: 0.7501 (p0) REVERT: B 294 TYR cc_start: 0.7082 (t80) cc_final: 0.6743 (t80) REVERT: C 54 ASN cc_start: 0.8319 (m110) cc_final: 0.8049 (m-40) REVERT: C 68 ARG cc_start: 0.8212 (ttt-90) cc_final: 0.7983 (ttt-90) REVERT: C 162 ASP cc_start: 0.8090 (p0) cc_final: 0.7799 (p0) REVERT: C 231 LEU cc_start: 0.7865 (OUTLIER) cc_final: 0.7660 (tt) REVERT: C 289 PHE cc_start: 0.7427 (t80) cc_final: 0.7043 (t80) REVERT: D 58 MET cc_start: 0.8447 (mmm) cc_final: 0.7837 (mtm) REVERT: D 112 MET cc_start: 0.8141 (tpp) cc_final: 0.7369 (tpp) REVERT: E 306 PHE cc_start: 0.7033 (OUTLIER) cc_final: 0.6757 (m-10) REVERT: J 65 GLN cc_start: 0.8118 (tp40) cc_final: 0.7905 (tp40) REVERT: J 80 TYR cc_start: 0.8924 (m-80) cc_final: 0.8618 (m-80) outliers start: 55 outliers final: 38 residues processed: 349 average time/residue: 0.3133 time to fit residues: 166.9342 Evaluate side-chains 343 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 303 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 90 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 10.0000 chunk 22 optimal weight: 0.1980 chunk 114 optimal weight: 0.0170 chunk 146 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 199 optimal weight: 8.9990 chunk 124 optimal weight: 9.9990 chunk 121 optimal weight: 0.7980 chunk 92 optimal weight: 0.3980 overall best weight: 0.4820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 189 ASN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 17799 Z= 0.154 Angle : 0.556 9.938 24204 Z= 0.275 Chirality : 0.043 0.389 2797 Planarity : 0.004 0.053 2981 Dihedral : 5.677 59.186 2783 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.60 % Allowed : 18.69 % Favored : 78.70 % 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: -0.30 (0.18), residues: 2103 helix: 1.51 (0.22), residues: 551 sheet: -0.58 (0.20), residues: 641 loop : -0.90 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP E 252 HIS 0.002 0.000 HIS B 102 PHE 0.026 0.001 PHE E 346 TYR 0.020 0.001 TYR A 338 ARG 0.012 0.000 ARG I 61 *********************** 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 368 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 319 time to evaluate : 1.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8428 (mtm110) cc_final: 0.8183 (mtm180) REVERT: A 319 TRP cc_start: 0.7328 (t60) cc_final: 0.6752 (t-100) REVERT: B 24 ASP cc_start: 0.7890 (t0) cc_final: 0.7481 (p0) REVERT: B 222 LYS cc_start: 0.8786 (mtmt) cc_final: 0.8320 (mtmt) REVERT: B 294 TYR cc_start: 0.7110 (t80) cc_final: 0.6732 (t80) REVERT: C 54 ASN cc_start: 0.8265 (m110) cc_final: 0.8028 (m-40) REVERT: C 68 ARG cc_start: 0.8209 (ttt-90) cc_final: 0.7977 (ttt-90) REVERT: C 212 PHE cc_start: 0.8742 (OUTLIER) cc_final: 0.8135 (m-80) REVERT: C 231 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7670 (tt) REVERT: C 289 PHE cc_start: 0.7498 (t80) cc_final: 0.6999 (t80) REVERT: D 112 MET cc_start: 0.8165 (tpp) cc_final: 0.7380 (tpp) REVERT: E 306 PHE cc_start: 0.6918 (OUTLIER) cc_final: 0.6641 (m-10) REVERT: J 65 GLN cc_start: 0.8092 (tp40) cc_final: 0.7889 (tp40) REVERT: J 80 TYR cc_start: 0.8979 (m-80) cc_final: 0.8673 (m-80) outliers start: 49 outliers final: 38 residues processed: 347 average time/residue: 0.2866 time to fit residues: 151.4026 Evaluate side-chains 350 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 309 time to evaluate : 2.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 189 ASN Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 90 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 5.9990 chunk 79 optimal weight: 0.1980 chunk 119 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 126 optimal weight: 0.5980 chunk 135 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 189 ASN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 189 ASN L 53 ASN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17799 Z= 0.167 Angle : 0.556 9.965 24204 Z= 0.275 Chirality : 0.043 0.394 2797 Planarity : 0.003 0.047 2981 Dihedral : 5.560 59.569 2783 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.81 % Allowed : 18.85 % Favored : 78.33 % 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: -0.15 (0.19), residues: 2103 helix: 1.60 (0.22), residues: 550 sheet: -0.43 (0.20), residues: 646 loop : -0.84 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP E 252 HIS 0.002 0.000 HIS B 142 PHE 0.016 0.001 PHE E 158 TYR 0.018 0.001 TYR A 338 ARG 0.010 0.000 ARG I 61 *********************** 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 366 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 313 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 ARG cc_start: 0.8422 (mtm110) cc_final: 0.8170 (mtm180) REVERT: A 319 TRP cc_start: 0.7333 (t60) cc_final: 0.6758 (t-100) REVERT: B 24 ASP cc_start: 0.7893 (t0) cc_final: 0.7476 (p0) REVERT: B 71 LYS cc_start: 0.8238 (tptp) cc_final: 0.8014 (tptm) REVERT: B 222 LYS cc_start: 0.8787 (mtmt) cc_final: 0.8311 (mtmt) REVERT: B 294 TYR cc_start: 0.7206 (t80) cc_final: 0.6815 (t80) REVERT: C 54 ASN cc_start: 0.8248 (m110) cc_final: 0.8034 (m-40) REVERT: C 68 ARG cc_start: 0.8205 (ttt-90) cc_final: 0.7977 (ttt-90) REVERT: C 212 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: C 231 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7608 (tt) REVERT: C 289 PHE cc_start: 0.7501 (t80) cc_final: 0.7005 (t80) REVERT: D 112 MET cc_start: 0.8171 (tpp) cc_final: 0.7414 (tpp) REVERT: E 306 PHE cc_start: 0.6843 (OUTLIER) cc_final: 0.6565 (m-10) REVERT: J 65 GLN cc_start: 0.8098 (tp40) cc_final: 0.7891 (tp40) REVERT: J 80 TYR cc_start: 0.8984 (m-80) cc_final: 0.8668 (m-80) outliers start: 53 outliers final: 47 residues processed: 343 average time/residue: 0.2868 time to fit residues: 149.3745 Evaluate side-chains 357 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 307 time to evaluate : 1.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 90 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 1.9990 chunk 191 optimal weight: 7.9990 chunk 174 optimal weight: 0.6980 chunk 185 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 168 optimal weight: 0.6980 chunk 175 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 189 ASN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17799 Z= 0.200 Angle : 0.562 9.747 24204 Z= 0.278 Chirality : 0.043 0.391 2797 Planarity : 0.003 0.045 2981 Dihedral : 5.513 59.614 2783 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.29 % Allowed : 18.96 % Favored : 77.75 % 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: -0.11 (0.19), residues: 2103 helix: 1.60 (0.22), residues: 549 sheet: -0.41 (0.20), residues: 646 loop : -0.78 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP E 252 HIS 0.003 0.001 HIS B 142 PHE 0.023 0.001 PHE E 346 TYR 0.017 0.001 TYR A 338 ARG 0.009 0.000 ARG I 61 *********************** 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 371 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 309 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 TRP cc_start: 0.7348 (t60) cc_final: 0.6785 (t-100) REVERT: B 24 ASP cc_start: 0.7911 (t0) cc_final: 0.7542 (p0) REVERT: B 222 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8311 (mtmt) REVERT: B 294 TYR cc_start: 0.7228 (t80) cc_final: 0.6831 (t80) REVERT: C 54 ASN cc_start: 0.8309 (m110) cc_final: 0.8086 (m-40) REVERT: C 68 ARG cc_start: 0.8202 (ttt-90) cc_final: 0.7972 (ttt-90) REVERT: C 212 PHE cc_start: 0.8745 (OUTLIER) cc_final: 0.8142 (m-80) REVERT: D 112 MET cc_start: 0.8180 (tpp) cc_final: 0.7439 (tpp) REVERT: E 306 PHE cc_start: 0.6866 (OUTLIER) cc_final: 0.6524 (m-10) REVERT: J 19 LYS cc_start: 0.8732 (tptp) cc_final: 0.8335 (tptp) REVERT: J 65 GLN cc_start: 0.8118 (tp40) cc_final: 0.7911 (tp40) outliers start: 62 outliers final: 51 residues processed: 346 average time/residue: 0.2857 time to fit residues: 150.0511 Evaluate side-chains 359 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 306 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 323 PHE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain B residue 243 VAL Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 81 MET Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 302 VAL Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 78 VAL Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 90 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 136 optimal weight: 0.0050 chunk 206 optimal weight: 0.9980 chunk 189 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 126 optimal weight: 0.0870 chunk 100 optimal weight: 3.9990 chunk 130 optimal weight: 7.9990 overall best weight: 0.8176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17799 Z= 0.181 Angle : 0.558 9.788 24204 Z= 0.276 Chirality : 0.043 0.395 2797 Planarity : 0.003 0.045 2981 Dihedral : 5.444 59.386 2783 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.87 % Allowed : 19.28 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.19), residues: 2103 helix: 1.51 (0.22), residues: 564 sheet: -0.40 (0.20), residues: 628 loop : -0.67 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP E 252 HIS 0.003 0.001 HIS B 142 PHE 0.030 0.001 PHE C 289 TYR 0.029 0.001 TYR B 294 ARG 0.009 0.000 ARG I 61 ********************** 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 365 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 311 time to evaluate : 1.908 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 TRP cc_start: 0.7316 (t60) cc_final: 0.6741 (t-100) REVERT: B 24 ASP cc_start: 0.7857 (t0) cc_final: 0.7528 (p0) REVERT: B 222 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8320 (mtmt) REVERT: B 246 TRP cc_start: 0.6832 (m100) cc_final: 0.6357 (m-10) REVERT: C 54 ASN cc_start: 0.8288 (m110) cc_final: 0.8072 (m-40) REVERT: C 68 ARG cc_start: 0.8204 (ttt-90) cc_final: 0.7978 (ttt-90) REVERT: C 212 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8214 (m-80) REVERT: D 112 MET cc_start: 0.8185 (tpp) cc_final: 0.7431 (tpp) REVERT: E 306 PHE cc_start: 0.6816 (OUTLIER) cc_final: 0.6410 (m-10) REVERT: E 343 PHE cc_start: 0.8614 (t80) cc_final: 0.8347 (t80) REVERT: J 19 LYS cc_start: 0.8650 (tptp) cc_final: 0.8255 (tptp) REVERT: J 107 TYR cc_start: 0.8417 (m-80) cc_final: 0.8161 (m-80) outliers start: 54 outliers final: 48 residues processed: 344 average time/residue: 0.2878 time to fit residues: 150.7079 Evaluate side-chains 351 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 301 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 142 ARG Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 205 SER Chi-restraints excluded: chain C residue 53 VAL Chi-restraints excluded: chain C residue 76 VAL Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 87 VAL Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 212 PHE Chi-restraints excluded: chain C residue 324 PHE Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain E residue 51 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 271 THR Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 306 PHE Chi-restraints excluded: chain I residue 65 SER Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 29 ILE Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 69 THR Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 90 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.1980 chunk 50 optimal weight: 0.5980 chunk 151 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 164 optimal weight: 0.9990 chunk 68 optimal weight: 0.2980 chunk 168 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 144 optimal weight: 1.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 189 ASN C 303 ASN L 53 ASN ** L 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.150703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115245 restraints weight = 21704.187| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.26 r_work: 0.3117 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17799 Z= 0.153 Angle : 0.549 10.979 24204 Z= 0.271 Chirality : 0.043 0.398 2797 Planarity : 0.003 0.045 2981 Dihedral : 5.349 59.761 2783 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 2.76 % Allowed : 19.54 % Favored : 77.70 % 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: 0.02 (0.19), residues: 2103 helix: 1.52 (0.22), residues: 567 sheet: -0.33 (0.20), residues: 628 loop : -0.61 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP E 252 HIS 0.003 0.000 HIS B 142 PHE 0.043 0.001 PHE E 346 TYR 0.034 0.001 TYR B 294 ARG 0.009 0.000 ARG I 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4314.73 seconds wall clock time: 79 minutes 14.51 seconds (4754.51 seconds total)