Starting phenix.real_space_refine on Sat Feb 17 03:51:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3w_22035/02_2024/6x3w_22035_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3w_22035/02_2024/6x3w_22035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3w_22035/02_2024/6x3w_22035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3w_22035/02_2024/6x3w_22035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3w_22035/02_2024/6x3w_22035_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3w_22035/02_2024/6x3w_22035_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 11235 2.51 5 N 2832 2.21 5 O 3235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C ARG 318": "NH1" <-> "NH2" Residue "C ARG 321": "NH1" <-> "NH2" Residue "D ARG 17": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D 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 GLU 209": "OE1" <-> "OE2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E ARG 176": "NH1" <-> "NH2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E ARG 197": "NH1" <-> "NH2" Residue "E ARG 207": "NH1" <-> "NH2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "E ARG 327": "NH1" <-> "NH2" Residue "I GLU 17": "OE1" <-> "OE2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "J GLU 42": "OE1" <-> "OE2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "J ARG 102": "NH1" <-> "NH2" Residue "L GLU 41": "OE1" <-> "OE2" Residue "L GLU 104": "OE1" <-> "OE2" Residue "K GLU 89": "OE1" <-> "OE2" Residue "K ARG 98": "NH1" <-> "NH2" Residue "K ARG 102": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 17399 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2729 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 116 Unusual residues: {'BMA': 1, 'MAN': 7, 'NAG': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 10 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 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: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'ABU': 1, 'NAG': 1, 'UQA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 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 Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'UQA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.71, per 1000 atoms: 0.56 Number of scatterers: 17399 At special positions: 0 Unit cell: (141.075, 127.875, 136.125, 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 3235 8.00 N 2832 7.00 C 11235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.02 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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 505 " - " 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: 7.07 Conformation dependent library (CDL) restraints added in 3.0 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: 34 helices and 28 sheets defined 28.1% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.35 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 219 through 241 removed outlier: 5.038A pdb=" N MET A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix removed outlier: 4.380A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TRP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 271 Processing helix chain 'A' and resid 280 through 304 Processing helix chain 'A' and resid 310 through 338 removed outlier: 3.586A pdb=" N ALA A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 224 through 246 removed outlier: 3.993A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix removed outlier: 4.117A pdb=" N SER B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TRP B 246 " --> pdb=" O GLN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 276 removed outlier: 3.750A pdb=" N SER B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 310 Processing helix chain 'B' and resid 315 through 344 removed outlier: 3.986A pdb=" N ALA B 319 " --> pdb=" O PRO B 315 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 219 through 241 removed outlier: 5.203A pdb=" N MET C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix removed outlier: 3.685A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 267 Processing helix chain 'C' and resid 280 through 304 Processing helix chain 'C' and resid 310 through 338 removed outlier: 3.662A 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 11 through 22 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 224 through 246 removed outlier: 3.840A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Proline residue: D 233 - end of helix removed outlier: 4.039A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.854A 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: 3.505A pdb=" N ARG D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.908A 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: 4.481A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 255 removed outlier: 5.545A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix removed outlier: 3.572A pdb=" N VAL E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER E 254 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE E 255 " --> pdb=" O SER E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 284 Processing helix chain 'E' and resid 297 through 323 removed outlier: 4.394A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 356 removed outlier: 4.745A pdb=" N LYS E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET E 331 " --> pdb=" O ARG E 327 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP E 332 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 4.035A 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: 6.316A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.573A 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: 3.816A pdb=" N CYS A 150 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.428A 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: 6.928A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 167 through 171 removed outlier: 6.176A pdb=" N THR B 39 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLU B 170 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL B 41 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 4.207A 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: 4.064A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.560A 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: 6.423A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.829A 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: 6.268A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 3.786A 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: 3.762A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.539A 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: 6.829A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 7.101A 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: 6.266A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 45 through 47 Processing sheet with id= L, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= M, first strand: chain 'D' and resid 150 through 154 removed outlier: 3.915A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 179 through 183 removed outlier: 5.733A pdb=" N THR E 51 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLN E 182 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE E 53 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 188 through 190 removed outlier: 6.622A pdb=" N MET E 57 " --> pdb=" O GLU E 189 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.617A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 116 through 121 removed outlier: 7.040A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 4 through 7 Processing sheet with id= S, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.473A pdb=" N LYS I 102 " --> pdb=" O MET I 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'I' and resid 85 through 90 removed outlier: 6.265A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 3 through 6 Processing sheet with id= V, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.517A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N TRP J 47 " --> pdb=" O LYS J 38 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= X, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.069A pdb=" N LYS L 102 " --> pdb=" O MET L 11 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N MET L 13 " --> pdb=" O LYS L 102 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLU L 104 " --> pdb=" O MET L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'L' and resid 85 through 90 removed outlier: 6.180A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 3 through 6 Processing sheet with id= AA, first strand: chain 'K' and resid 10 through 12 Processing sheet with id= AB, first strand: chain 'K' and resid 57 through 60 removed outlier: 3.671A pdb=" N ASP K 57 " --> pdb=" O ASP K 52 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N TYR K 33 " --> pdb=" O LYS K 99 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 739 hydrogen bonds defined for protein. 2157 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: 5.30 Time building geometry restraints manager: 7.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4373 1.33 - 1.46: 4820 1.46 - 1.58: 8475 1.58 - 1.71: 0 1.71 - 1.83: 167 Bond restraints: 17835 Sorted by residual: bond pdb=" CD ABU A 405 " pdb=" OE2 ABU A 405 " ideal model delta sigma weight residual 1.250 1.333 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" CD ABU C 506 " pdb=" OE2 ABU C 506 " ideal model delta sigma weight residual 1.250 1.333 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C MET D 114 " pdb=" N PRO D 115 " ideal model delta sigma weight residual 1.332 1.374 -0.042 1.12e-02 7.97e+03 1.41e+01 bond pdb=" C VAL D 252 " pdb=" N PRO D 253 " ideal model delta sigma weight residual 1.335 1.373 -0.039 1.28e-02 6.10e+03 9.07e+00 bond pdb=" C THR E 125 " pdb=" N THR E 126 " ideal model delta sigma weight residual 1.333 1.292 0.042 1.39e-02 5.18e+03 8.99e+00 ... (remaining 17830 not shown) Histogram of bond angle deviations from ideal: 95.19 - 103.08: 129 103.08 - 110.98: 6275 110.98 - 118.88: 7974 118.88 - 126.77: 9615 126.77 - 134.67: 263 Bond angle restraints: 24256 Sorted by residual: angle pdb=" N ARG C 269 " pdb=" CA ARG C 269 " pdb=" C ARG C 269 " ideal model delta sigma weight residual 113.41 104.73 8.68 1.22e+00 6.72e-01 5.07e+01 angle pdb=" C THR C 271 " pdb=" N LEU C 272 " pdb=" CA LEU C 272 " ideal model delta sigma weight residual 123.96 133.94 -9.98 1.44e+00 4.82e-01 4.80e+01 angle pdb=" N ILE C 322 " pdb=" CA ILE C 322 " pdb=" C ILE C 322 " ideal model delta sigma weight residual 112.96 107.97 4.99 1.00e+00 1.00e+00 2.49e+01 angle pdb=" CA GLU C 147 " pdb=" CB GLU C 147 " pdb=" CG GLU C 147 " ideal model delta sigma weight residual 114.10 123.27 -9.17 2.00e+00 2.50e-01 2.10e+01 angle pdb=" N LEU C 152 " pdb=" CA LEU C 152 " pdb=" C LEU C 152 " ideal model delta sigma weight residual 108.34 100.95 7.39 1.64e+00 3.72e-01 2.03e+01 ... (remaining 24251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.87: 10093 21.87 - 43.73: 601 43.73 - 65.60: 64 65.60 - 87.47: 34 87.47 - 109.33: 14 Dihedral angle restraints: 10806 sinusoidal: 4550 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 -9.25 -76.75 1 1.00e+01 1.00e-02 7.40e+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 -12.15 -73.85 1 1.00e+01 1.00e-02 6.93e+01 dihedral pdb=" CA CYS C 150 " pdb=" C CYS C 150 " pdb=" N THR C 151 " pdb=" CA THR C 151 " ideal model delta harmonic sigma weight residual -180.00 -151.89 -28.11 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 10803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.283: 2784 0.283 - 0.565: 9 0.565 - 0.848: 4 0.848 - 1.130: 1 1.130 - 1.413: 1 Chirality restraints: 2799 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.99 -1.41 2.00e-02 2.50e+03 4.99e+03 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-02 2.50e+03 1.52e+03 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 1.64 0.76 2.00e-02 2.50e+03 1.46e+03 ... (remaining 2796 not shown) Planarity restraints: 2992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " 0.193 2.00e-02 2.50e+03 1.59e-01 3.17e+02 pdb=" C7 NAG M 2 " -0.052 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " 0.140 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " -0.258 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " -0.180 2.00e-02 2.50e+03 1.53e-01 2.93e+02 pdb=" C7 NAG M 1 " 0.037 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " 0.036 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " 0.249 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " -0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " -0.129 2.00e-02 2.50e+03 1.06e-01 1.41e+02 pdb=" C7 NAG G 2 " 0.034 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " -0.096 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " 0.171 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " 0.020 2.00e-02 2.50e+03 ... (remaining 2989 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1981 2.75 - 3.29: 15940 3.29 - 3.82: 29721 3.82 - 4.36: 36301 4.36 - 4.90: 63788 Nonbonded interactions: 147731 Sorted by model distance: nonbonded pdb=" OD1 ASP E 120 " pdb=" O4 MAN G 10 " model vdw 2.211 2.440 nonbonded pdb=" OD2 ASP A 121 " pdb=" OG1 THR A 123 " model vdw 2.269 2.440 nonbonded pdb=" O ALA E 295 " pdb=" OH TYR E 350 " model vdw 2.281 2.440 nonbonded pdb=" OH TYR D 26 " pdb=" OD2 ASP D 72 " model vdw 2.283 2.440 nonbonded pdb=" OG1 THR B 99 " pdb=" OH TYR B 169 " model vdw 2.289 2.440 ... (remaining 147726 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' and resid 7 through 340) selection = (chain 'C' and resid 7 through 340) } 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: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 5.520 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 48.570 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.120 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 17835 Z= 0.509 Angle : 1.158 13.492 24256 Z= 0.640 Chirality : 0.082 1.413 2799 Planarity : 0.008 0.159 2985 Dihedral : 14.582 109.332 6759 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.85 % Allowed : 6.80 % Favored : 92.35 % Cbeta Deviations : 0.05 % 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: -2.06 (0.16), residues: 2103 helix: -0.16 (0.20), residues: 581 sheet: -1.01 (0.19), residues: 623 loop : -2.41 (0.17), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP K 103 HIS 0.008 0.002 HIS D 56 PHE 0.031 0.004 PHE C 221 TYR 0.040 0.003 TYR A 157 ARG 0.009 0.001 ARG D 85 *********************** 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 427 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 411 time to evaluate : 2.019 Fit side-chains revert: symmetry clash REVERT: A 95 ASP cc_start: 0.8036 (p0) cc_final: 0.7053 (t0) REVERT: A 142 ARG cc_start: 0.7557 (mtp180) cc_final: 0.7157 (mtt180) REVERT: A 274 LYS cc_start: 0.7994 (mttt) cc_final: 0.7761 (mttm) REVERT: A 323 PHE cc_start: 0.7139 (t80) cc_final: 0.6765 (t80) REVERT: C 52 GLU cc_start: 0.7965 (mp0) cc_final: 0.7668 (mp0) REVERT: C 142 ARG cc_start: 0.7661 (mtp180) cc_final: 0.7411 (mtp85) REVERT: C 303 ASN cc_start: 0.8725 (t0) cc_final: 0.8518 (t0) REVERT: D 93 LYS cc_start: 0.8503 (tptp) cc_final: 0.7776 (tptp) REVERT: D 98 ASP cc_start: 0.8287 (p0) cc_final: 0.8048 (p0) REVERT: D 156 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8195 (mtmt) REVERT: E 296 MET cc_start: 0.7496 (ttp) cc_final: 0.7282 (ttp) REVERT: E 298 LEU cc_start: 0.8952 (tp) cc_final: 0.8721 (tt) REVERT: E 301 SER cc_start: 0.8822 (m) cc_final: 0.8179 (m) REVERT: E 305 ILE cc_start: 0.8045 (mm) cc_final: 0.7610 (mm) REVERT: E 337 ILE cc_start: 0.8683 (tp) cc_final: 0.8421 (tp) outliers start: 16 outliers final: 10 residues processed: 421 average time/residue: 0.3292 time to fit residues: 199.4187 Evaluate side-chains 341 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 331 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 274 LEU 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: 4.9990 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 162 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 65 GLN A 185 GLN A 303 ASN B 68 GLN B 142 HIS B 189 ASN B 275 ASN B 308 ASN C 41 ASN C 54 ASN C 65 GLN C 303 ASN D 68 GLN D 102 HIS E 60 ASN E 80 GLN E 128 ASN E 163 HIS E 258 ASN E 318 HIS J 6 GLN L 42 GLN K 6 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17835 Z= 0.218 Angle : 0.581 9.482 24256 Z= 0.295 Chirality : 0.044 0.245 2799 Planarity : 0.004 0.039 2985 Dihedral : 8.257 77.516 2830 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.07 % Allowed : 11.79 % Favored : 86.14 % 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: -1.30 (0.17), residues: 2103 helix: 0.51 (0.21), residues: 585 sheet: -0.83 (0.18), residues: 641 loop : -1.78 (0.19), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 103 HIS 0.005 0.001 HIS B 142 PHE 0.018 0.001 PHE D 310 TYR 0.022 0.001 TYR A 299 ARG 0.007 0.001 ARG K 102 *********************** 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 395 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 356 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7598 (mtp180) cc_final: 0.7175 (mtt180) REVERT: A 323 PHE cc_start: 0.7112 (t80) cc_final: 0.6660 (t80) REVERT: B 24 ASP cc_start: 0.6856 (t0) cc_final: 0.6595 (p0) REVERT: B 202 ILE cc_start: 0.9083 (mm) cc_final: 0.8813 (mt) REVERT: B 266 MET cc_start: 0.8889 (mmm) cc_final: 0.8651 (mmm) REVERT: C 52 GLU cc_start: 0.7966 (mp0) cc_final: 0.7677 (mp0) REVERT: D 93 LYS cc_start: 0.8516 (tptp) cc_final: 0.8063 (mmmm) REVERT: D 156 LYS cc_start: 0.8478 (mtmm) cc_final: 0.8007 (mtpt) REVERT: E 296 MET cc_start: 0.7515 (ttp) cc_final: 0.7222 (ttp) REVERT: E 301 SER cc_start: 0.8808 (m) cc_final: 0.8223 (m) REVERT: E 305 ILE cc_start: 0.8222 (mm) cc_final: 0.7768 (mm) REVERT: E 337 ILE cc_start: 0.8653 (tp) cc_final: 0.8344 (tp) REVERT: I 13 MET cc_start: 0.4564 (OUTLIER) cc_final: 0.4129 (ppp) REVERT: K 5 GLN cc_start: 0.7425 (tm-30) cc_final: 0.7078 (tm-30) REVERT: K 102 ARG cc_start: 0.8594 (mmm-85) cc_final: 0.8275 (mmm-85) outliers start: 39 outliers final: 32 residues processed: 375 average time/residue: 0.3251 time to fit residues: 178.9497 Evaluate side-chains 361 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 328 time to evaluate : 2.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 243 ASN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 87 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 156 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 188 optimal weight: 7.9990 chunk 203 optimal weight: 8.9990 chunk 167 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 64 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 185 GLN B 116 ASN C 54 ASN D 88 ASN E 200 GLN E 318 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17835 Z= 0.237 Angle : 0.562 9.631 24256 Z= 0.284 Chirality : 0.044 0.261 2799 Planarity : 0.004 0.037 2985 Dihedral : 6.607 64.673 2823 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.56 % Allowed : 13.06 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.17), residues: 2103 helix: 0.87 (0.21), residues: 587 sheet: -0.84 (0.19), residues: 623 loop : -1.36 (0.19), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 103 HIS 0.004 0.001 HIS B 142 PHE 0.013 0.001 PHE A 221 TYR 0.024 0.001 TYR A 191 ARG 0.007 0.000 ARG C 68 *********************** 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 400 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 333 time to evaluate : 2.047 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7713 (mtp180) cc_final: 0.7161 (mtt180) REVERT: A 191 TYR cc_start: 0.8533 (p90) cc_final: 0.8294 (p90) REVERT: A 323 PHE cc_start: 0.7150 (t80) cc_final: 0.6598 (t80) REVERT: B 24 ASP cc_start: 0.6950 (t0) cc_final: 0.6722 (p0) REVERT: B 112 MET cc_start: 0.8200 (tpp) cc_final: 0.7944 (tpp) REVERT: B 131 MET cc_start: 0.8605 (mtp) cc_final: 0.8401 (mtp) REVERT: B 240 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.7552 (tp) REVERT: B 258 PHE cc_start: 0.8330 (OUTLIER) cc_final: 0.7123 (t80) REVERT: D 15 PHE cc_start: 0.8527 (m-80) cc_final: 0.8087 (m-80) REVERT: D 21 ARG cc_start: 0.7128 (ttp-110) cc_final: 0.6838 (ttp-110) REVERT: D 93 LYS cc_start: 0.8552 (tptp) cc_final: 0.8025 (mmmm) REVERT: D 156 LYS cc_start: 0.8506 (mtmm) cc_final: 0.8169 (mtmt) REVERT: E 289 LYS cc_start: 0.8418 (mttm) cc_final: 0.8136 (mttt) REVERT: E 296 MET cc_start: 0.7426 (ttp) cc_final: 0.7108 (ttp) REVERT: E 301 SER cc_start: 0.8762 (m) cc_final: 0.8273 (m) REVERT: E 305 ILE cc_start: 0.8344 (mm) cc_final: 0.7932 (mm) REVERT: E 337 ILE cc_start: 0.8650 (tp) cc_final: 0.8343 (tp) REVERT: E 356 TYR cc_start: 0.5218 (OUTLIER) cc_final: 0.5016 (t80) REVERT: I 13 MET cc_start: 0.4750 (OUTLIER) cc_final: 0.4316 (ppp) REVERT: L 4 MET cc_start: 0.8336 (mmm) cc_final: 0.8071 (mtp) REVERT: K 5 GLN cc_start: 0.7472 (tm-30) cc_final: 0.7120 (tm-30) REVERT: K 80 TYR cc_start: 0.8548 (m-80) cc_final: 0.8273 (m-80) REVERT: K 102 ARG cc_start: 0.8651 (mmm-85) cc_final: 0.8227 (mmm-85) outliers start: 67 outliers final: 48 residues processed: 372 average time/residue: 0.3166 time to fit residues: 173.2730 Evaluate side-chains 367 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 315 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 115 MET Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 229 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 243 ASN Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 131 MET 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 258 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 157 ASN Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 110 GLN Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 0.0030 chunk 141 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 188 optimal weight: 2.9990 chunk 200 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.9196 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17835 Z= 0.190 Angle : 0.531 9.540 24256 Z= 0.268 Chirality : 0.042 0.254 2799 Planarity : 0.004 0.037 2985 Dihedral : 6.070 58.071 2822 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.29 % Allowed : 14.39 % Favored : 82.32 % 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: -0.63 (0.18), residues: 2103 helix: 1.17 (0.22), residues: 575 sheet: -0.76 (0.19), residues: 625 loop : -1.13 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 103 HIS 0.004 0.001 HIS B 142 PHE 0.023 0.001 PHE D 310 TYR 0.023 0.001 TYR A 299 ARG 0.006 0.000 ARG C 141 *********************** 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 381 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 319 time to evaluate : 1.955 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7714 (mtp180) cc_final: 0.7282 (mtt180) REVERT: A 191 TYR cc_start: 0.8616 (p90) cc_final: 0.8355 (p90) REVERT: A 323 PHE cc_start: 0.7178 (t80) cc_final: 0.6545 (t80) REVERT: B 112 MET cc_start: 0.8205 (tpp) cc_final: 0.7956 (tpp) REVERT: B 240 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.7655 (tp) REVERT: B 258 PHE cc_start: 0.8287 (OUTLIER) cc_final: 0.7181 (t80) REVERT: C 142 ARG cc_start: 0.7990 (mtp-110) cc_final: 0.7699 (mtp-110) REVERT: D 21 ARG cc_start: 0.7158 (ttp-110) cc_final: 0.6900 (ttp-110) REVERT: D 93 LYS cc_start: 0.8506 (tptp) cc_final: 0.7975 (mmmm) REVERT: D 156 LYS cc_start: 0.8486 (mtmm) cc_final: 0.8165 (mtmt) REVERT: E 178 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7677 (mt-10) REVERT: E 289 LYS cc_start: 0.8419 (mttm) cc_final: 0.8114 (mttt) REVERT: E 296 MET cc_start: 0.7389 (ttp) cc_final: 0.6957 (ttp) REVERT: E 301 SER cc_start: 0.8759 (m) cc_final: 0.8283 (m) REVERT: E 305 ILE cc_start: 0.8350 (mm) cc_final: 0.7937 (mm) REVERT: E 337 ILE cc_start: 0.8646 (tp) cc_final: 0.8358 (tp) REVERT: E 356 TYR cc_start: 0.5226 (OUTLIER) cc_final: 0.4998 (t80) REVERT: I 13 MET cc_start: 0.4827 (OUTLIER) cc_final: 0.4457 (ppp) REVERT: J 112 THR cc_start: 0.8891 (OUTLIER) cc_final: 0.8621 (t) REVERT: K 5 GLN cc_start: 0.7445 (tm-30) cc_final: 0.7088 (tm-30) REVERT: K 102 ARG cc_start: 0.8578 (mmm-85) cc_final: 0.8199 (mmm-85) outliers start: 62 outliers final: 48 residues processed: 355 average time/residue: 0.3033 time to fit residues: 160.1372 Evaluate side-chains 363 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 310 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 243 ASN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 131 MET 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 258 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain J residue 112 THR Chi-restraints excluded: chain J residue 113 SER Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain K residue 20 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 148 optimal weight: 0.8980 chunk 82 optimal weight: 0.0030 chunk 170 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 179 optimal weight: 8.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 224 GLN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN D 88 ASN E 318 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17835 Z= 0.191 Angle : 0.523 9.559 24256 Z= 0.264 Chirality : 0.042 0.251 2799 Planarity : 0.004 0.039 2985 Dihedral : 5.756 55.267 2822 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.72 % Allowed : 15.08 % 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: -0.41 (0.18), residues: 2103 helix: 1.29 (0.22), residues: 575 sheet: -0.69 (0.19), residues: 635 loop : -0.90 (0.20), residues: 893 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 319 HIS 0.005 0.001 HIS B 142 PHE 0.016 0.001 PHE D 310 TYR 0.023 0.001 TYR A 299 ARG 0.009 0.000 ARG B 17 *********************** 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 392 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 322 time to evaluate : 1.751 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7785 (mtp180) cc_final: 0.7336 (mtt180) REVERT: A 191 TYR cc_start: 0.8650 (p90) cc_final: 0.8390 (p90) REVERT: A 323 PHE cc_start: 0.7161 (t80) cc_final: 0.6510 (t80) REVERT: B 112 MET cc_start: 0.8230 (tpp) cc_final: 0.7983 (tpp) REVERT: B 240 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.7685 (tp) REVERT: B 258 PHE cc_start: 0.8276 (OUTLIER) cc_final: 0.7175 (t80) REVERT: D 21 ARG cc_start: 0.7163 (ttp-110) cc_final: 0.6862 (ttp-110) REVERT: D 93 LYS cc_start: 0.8553 (tptp) cc_final: 0.8035 (mmmm) REVERT: D 98 ASP cc_start: 0.8400 (p0) cc_final: 0.8132 (p0) REVERT: D 156 LYS cc_start: 0.8483 (mtmm) cc_final: 0.8162 (mtmt) REVERT: E 178 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7665 (mt-10) REVERT: E 289 LYS cc_start: 0.8433 (mttm) cc_final: 0.8128 (mttt) REVERT: E 296 MET cc_start: 0.7368 (ttp) cc_final: 0.6965 (ttp) REVERT: E 301 SER cc_start: 0.8765 (m) cc_final: 0.8282 (m) REVERT: E 305 ILE cc_start: 0.8349 (mm) cc_final: 0.7950 (mm) REVERT: E 337 ILE cc_start: 0.8653 (tp) cc_final: 0.8334 (tp) REVERT: E 356 TYR cc_start: 0.5346 (OUTLIER) cc_final: 0.5053 (t80) REVERT: I 13 MET cc_start: 0.4737 (OUTLIER) cc_final: 0.4337 (ppp) REVERT: K 102 ARG cc_start: 0.8582 (mmm-85) cc_final: 0.8252 (mmm-85) outliers start: 70 outliers final: 58 residues processed: 361 average time/residue: 0.2857 time to fit residues: 155.4116 Evaluate side-chains 378 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 316 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 240 LEU Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 243 ASN Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 131 MET 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 258 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 200 optimal weight: 0.5980 chunk 166 optimal weight: 0.0980 chunk 92 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 224 GLN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN E 318 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17835 Z= 0.165 Angle : 0.514 9.553 24256 Z= 0.260 Chirality : 0.042 0.249 2799 Planarity : 0.003 0.039 2985 Dihedral : 5.599 55.873 2822 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.77 % Allowed : 15.51 % Favored : 80.72 % 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: -0.27 (0.18), residues: 2103 helix: 1.34 (0.22), residues: 580 sheet: -0.63 (0.19), residues: 636 loop : -0.75 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 319 HIS 0.004 0.000 HIS B 142 PHE 0.014 0.001 PHE D 310 TYR 0.023 0.001 TYR A 299 ARG 0.006 0.000 ARG B 17 *********************** 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 400 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 329 time to evaluate : 2.048 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7797 (mtp180) cc_final: 0.7400 (mtt180) REVERT: A 191 TYR cc_start: 0.8643 (p90) cc_final: 0.8385 (p90) REVERT: A 286 MET cc_start: 0.6977 (mtt) cc_final: 0.6695 (mtt) REVERT: A 323 PHE cc_start: 0.7174 (t80) cc_final: 0.6488 (t80) REVERT: B 112 MET cc_start: 0.8224 (tpp) cc_final: 0.7975 (tpp) REVERT: C 142 ARG cc_start: 0.7994 (mtp-110) cc_final: 0.7698 (mtp-110) REVERT: C 322 ILE cc_start: 0.8397 (OUTLIER) cc_final: 0.7674 (mm) REVERT: D 21 ARG cc_start: 0.7137 (ttp-110) cc_final: 0.6858 (ttp-110) REVERT: D 93 LYS cc_start: 0.8548 (tptp) cc_final: 0.8166 (mmmt) REVERT: D 98 ASP cc_start: 0.8324 (p0) cc_final: 0.8037 (p0) REVERT: D 156 LYS cc_start: 0.8464 (mtmm) cc_final: 0.8155 (mtmt) REVERT: E 178 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7660 (mt-10) REVERT: E 296 MET cc_start: 0.7310 (ttp) cc_final: 0.6873 (ttp) REVERT: E 301 SER cc_start: 0.8744 (m) cc_final: 0.8306 (m) REVERT: E 305 ILE cc_start: 0.8352 (mm) cc_final: 0.7959 (mm) REVERT: E 337 ILE cc_start: 0.8655 (tp) cc_final: 0.8338 (tp) REVERT: E 356 TYR cc_start: 0.5271 (OUTLIER) cc_final: 0.4998 (t80) REVERT: I 13 MET cc_start: 0.4706 (OUTLIER) cc_final: 0.4353 (ppp) REVERT: K 102 ARG cc_start: 0.8562 (mmm-85) cc_final: 0.8239 (mmm-85) outliers start: 71 outliers final: 56 residues processed: 369 average time/residue: 0.2978 time to fit residues: 164.2662 Evaluate side-chains 374 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 315 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 131 MET Chi-restraints excluded: chain D residue 197 THR Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain D residue 243 VAL Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain I residue 103 LEU Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 146 optimal weight: 0.0980 chunk 113 optimal weight: 0.9990 chunk 168 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 199 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 121 optimal weight: 3.9990 chunk 92 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 224 GLN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN C 41 ASN D 87 ASN E 318 HIS K 3 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17835 Z= 0.191 Angle : 0.519 9.555 24256 Z= 0.263 Chirality : 0.042 0.249 2799 Planarity : 0.003 0.039 2985 Dihedral : 5.454 55.993 2822 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.93 % Allowed : 15.88 % Favored : 80.19 % 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: -0.19 (0.18), residues: 2103 helix: 1.40 (0.22), residues: 580 sheet: -0.61 (0.19), residues: 637 loop : -0.68 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 319 HIS 0.004 0.001 HIS B 142 PHE 0.011 0.001 PHE A 323 TYR 0.022 0.001 TYR A 299 ARG 0.007 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 327 time to evaluate : 1.918 Fit side-chains revert: symmetry clash REVERT: A 79 LEU cc_start: 0.8920 (pt) cc_final: 0.8632 (pp) REVERT: A 142 ARG cc_start: 0.7816 (mtp180) cc_final: 0.7397 (mtt180) REVERT: A 191 TYR cc_start: 0.8658 (p90) cc_final: 0.8417 (p90) REVERT: A 286 MET cc_start: 0.6985 (mtt) cc_final: 0.6705 (mtt) REVERT: A 323 PHE cc_start: 0.7110 (t80) cc_final: 0.6425 (t80) REVERT: B 112 MET cc_start: 0.8244 (tpp) cc_final: 0.8005 (tpp) REVERT: B 279 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8276 (mttm) REVERT: C 142 ARG cc_start: 0.8008 (mtp-110) cc_final: 0.7710 (mtp-110) REVERT: C 322 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.7707 (mm) REVERT: D 21 ARG cc_start: 0.7142 (ttp-110) cc_final: 0.6881 (ttp-110) REVERT: D 93 LYS cc_start: 0.8553 (tptp) cc_final: 0.8164 (mmmt) REVERT: D 156 LYS cc_start: 0.8474 (mtmm) cc_final: 0.8168 (mtmt) REVERT: D 261 THR cc_start: 0.8466 (m) cc_final: 0.7996 (t) REVERT: E 178 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7618 (mt-10) REVERT: E 301 SER cc_start: 0.8758 (m) cc_final: 0.8324 (m) REVERT: E 305 ILE cc_start: 0.8363 (mm) cc_final: 0.7971 (mm) REVERT: E 337 ILE cc_start: 0.8665 (tp) cc_final: 0.8356 (tp) REVERT: E 356 TYR cc_start: 0.5347 (OUTLIER) cc_final: 0.5013 (t80) REVERT: I 13 MET cc_start: 0.4792 (OUTLIER) cc_final: 0.4372 (ppp) REVERT: I 79 GLN cc_start: 0.8087 (mp10) cc_final: 0.7173 (mp10) REVERT: L 79 GLN cc_start: 0.7390 (mp10) cc_final: 0.7046 (mp10) REVERT: K 102 ARG cc_start: 0.8587 (mmm-85) cc_final: 0.8358 (mmm-85) outliers start: 74 outliers final: 54 residues processed: 372 average time/residue: 0.3005 time to fit residues: 168.1063 Evaluate side-chains 379 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 321 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 275 ILE Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 279 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 131 MET 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 258 PHE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 87 THR 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 L residue 14 SER Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.9980 chunk 79 optimal weight: 0.0000 chunk 119 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 156 optimal weight: 6.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 ASN A 185 GLN A 224 GLN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 41 ASN E 318 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17835 Z= 0.163 Angle : 0.511 9.546 24256 Z= 0.258 Chirality : 0.042 0.248 2799 Planarity : 0.003 0.040 2985 Dihedral : 5.331 56.341 2822 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.19 % Allowed : 16.57 % Favored : 80.24 % 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: -0.09 (0.18), residues: 2103 helix: 1.50 (0.22), residues: 580 sheet: -0.44 (0.19), residues: 638 loop : -0.72 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 241 HIS 0.003 0.000 HIS B 142 PHE 0.011 0.001 PHE A 323 TYR 0.021 0.001 TYR A 299 ARG 0.007 0.000 ARG B 164 *********************** 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 394 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 334 time to evaluate : 1.953 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7791 (mtp180) cc_final: 0.7374 (mtt180) REVERT: A 191 TYR cc_start: 0.8627 (p90) cc_final: 0.8407 (p90) REVERT: A 286 MET cc_start: 0.6991 (mtt) cc_final: 0.6713 (mtt) REVERT: A 294 MET cc_start: 0.8016 (mmm) cc_final: 0.7816 (mmm) REVERT: A 323 PHE cc_start: 0.7078 (t80) cc_final: 0.6399 (t80) REVERT: B 17 ARG cc_start: 0.8104 (mtm-85) cc_final: 0.7735 (mtt-85) REVERT: B 112 MET cc_start: 0.8267 (tpp) cc_final: 0.7999 (tpp) REVERT: B 279 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8255 (mttm) REVERT: B 323 ARG cc_start: 0.7986 (ttp80) cc_final: 0.7665 (ttp80) REVERT: C 142 ARG cc_start: 0.8023 (mtp-110) cc_final: 0.7743 (mtp-110) REVERT: C 322 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.7719 (mm) REVERT: D 15 PHE cc_start: 0.8440 (m-80) cc_final: 0.8107 (m-80) REVERT: D 21 ARG cc_start: 0.7137 (ttp-110) cc_final: 0.6882 (ttp-110) REVERT: D 93 LYS cc_start: 0.8541 (tptp) cc_final: 0.7967 (mmmm) REVERT: D 156 LYS cc_start: 0.8445 (mtmm) cc_final: 0.8145 (mtmt) REVERT: D 261 THR cc_start: 0.8421 (m) cc_final: 0.7953 (t) REVERT: E 178 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7619 (mt-10) REVERT: E 296 MET cc_start: 0.7353 (ttp) cc_final: 0.7105 (ttp) REVERT: E 301 SER cc_start: 0.8774 (m) cc_final: 0.8355 (m) REVERT: E 305 ILE cc_start: 0.8356 (mm) cc_final: 0.7973 (mm) REVERT: E 337 ILE cc_start: 0.8664 (tp) cc_final: 0.8357 (tp) REVERT: E 356 TYR cc_start: 0.5343 (OUTLIER) cc_final: 0.5003 (t80) REVERT: I 13 MET cc_start: 0.4780 (OUTLIER) cc_final: 0.4424 (ppp) REVERT: L 60 ASP cc_start: 0.7603 (t0) cc_final: 0.7270 (t70) REVERT: L 79 GLN cc_start: 0.7413 (mp10) cc_final: 0.7082 (mp10) REVERT: K 102 ARG cc_start: 0.8573 (mmm-85) cc_final: 0.8326 (mmm-85) outliers start: 60 outliers final: 52 residues processed: 365 average time/residue: 0.2933 time to fit residues: 160.6083 Evaluate side-chains 380 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 324 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 279 LYS Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 322 ILE Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 131 MET 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 258 PHE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 11 MET Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 90 ASP 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 L residue 14 SER Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 10.0000 chunk 191 optimal weight: 9.9990 chunk 174 optimal weight: 2.9990 chunk 185 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 145 optimal weight: 0.1980 chunk 57 optimal weight: 0.1980 chunk 168 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 224 GLN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN C 41 ASN C 224 GLN E 318 HIS L 37 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17835 Z= 0.222 Angle : 0.538 9.549 24256 Z= 0.272 Chirality : 0.043 0.250 2799 Planarity : 0.004 0.042 2985 Dihedral : 5.341 55.693 2822 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 3.66 % Allowed : 16.83 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.18), residues: 2103 helix: 1.52 (0.22), residues: 579 sheet: -0.39 (0.20), residues: 626 loop : -0.64 (0.21), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 241 HIS 0.003 0.001 HIS B 142 PHE 0.012 0.001 PHE B 226 TYR 0.022 0.001 TYR A 299 ARG 0.007 0.000 ARG C 68 *********************** 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 397 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 328 time to evaluate : 2.044 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7824 (mtp180) cc_final: 0.7334 (mtt180) REVERT: A 191 TYR cc_start: 0.8662 (p90) cc_final: 0.8421 (p90) REVERT: A 286 MET cc_start: 0.7026 (mtt) cc_final: 0.6763 (mtt) REVERT: A 294 MET cc_start: 0.8049 (mmm) cc_final: 0.7830 (mmm) REVERT: B 17 ARG cc_start: 0.8094 (mtm-85) cc_final: 0.7662 (mtt90) REVERT: B 112 MET cc_start: 0.8250 (tpp) cc_final: 0.7980 (tpp) REVERT: C 142 ARG cc_start: 0.8079 (mtp-110) cc_final: 0.7777 (mtp-110) REVERT: D 15 PHE cc_start: 0.8475 (m-80) cc_final: 0.8139 (m-80) REVERT: D 21 ARG cc_start: 0.7127 (ttp-110) cc_final: 0.6873 (ttp-110) REVERT: D 93 LYS cc_start: 0.8567 (tptp) cc_final: 0.7970 (mmmm) REVERT: D 156 LYS cc_start: 0.8481 (mtmm) cc_final: 0.8172 (mtmt) REVERT: D 261 THR cc_start: 0.8428 (m) cc_final: 0.7984 (t) REVERT: E 296 MET cc_start: 0.7412 (ttp) cc_final: 0.7169 (ttp) REVERT: E 301 SER cc_start: 0.8781 (m) cc_final: 0.8378 (m) REVERT: E 305 ILE cc_start: 0.8382 (mm) cc_final: 0.8024 (mm) REVERT: E 337 ILE cc_start: 0.8667 (tp) cc_final: 0.8367 (tp) REVERT: E 356 TYR cc_start: 0.5384 (OUTLIER) cc_final: 0.5016 (t80) REVERT: I 13 MET cc_start: 0.4825 (OUTLIER) cc_final: 0.4437 (ppp) REVERT: I 90 GLN cc_start: 0.9296 (pp30) cc_final: 0.9065 (pp30) REVERT: L 60 ASP cc_start: 0.7635 (t0) cc_final: 0.7331 (t70) REVERT: K 102 ARG cc_start: 0.8679 (mmm-85) cc_final: 0.8455 (mmm-85) outliers start: 69 outliers final: 59 residues processed: 364 average time/residue: 0.3146 time to fit residues: 170.7477 Evaluate side-chains 380 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 319 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 131 MET 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 258 PHE Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 90 ASP 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 L residue 14 SER Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 118 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 206 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 126 optimal weight: 0.0470 chunk 100 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 224 GLN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 HIS J 43 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17835 Z= 0.165 Angle : 0.517 9.525 24256 Z= 0.261 Chirality : 0.042 0.249 2799 Planarity : 0.003 0.039 2985 Dihedral : 5.248 56.409 2822 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.03 % Allowed : 17.31 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.19), residues: 2103 helix: 1.60 (0.22), residues: 579 sheet: -0.40 (0.20), residues: 638 loop : -0.62 (0.21), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 241 HIS 0.002 0.000 HIS D 110 PHE 0.011 0.001 PHE B 157 TYR 0.022 0.001 TYR A 299 ARG 0.007 0.000 ARG C 68 ********************** 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 384 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 327 time to evaluate : 1.901 Fit side-chains revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7803 (mtp180) cc_final: 0.7396 (mtt180) REVERT: A 191 TYR cc_start: 0.8634 (p90) cc_final: 0.8400 (p90) REVERT: A 286 MET cc_start: 0.6989 (mtt) cc_final: 0.6718 (mtt) REVERT: A 294 MET cc_start: 0.8035 (mmm) cc_final: 0.7817 (mmm) REVERT: B 17 ARG cc_start: 0.8072 (mtm-85) cc_final: 0.7656 (mtt90) REVERT: B 112 MET cc_start: 0.8265 (tpp) cc_final: 0.7965 (tpp) REVERT: C 142 ARG cc_start: 0.8046 (mtp-110) cc_final: 0.7768 (mtp-110) REVERT: D 15 PHE cc_start: 0.8455 (m-80) cc_final: 0.8095 (m-80) REVERT: D 21 ARG cc_start: 0.7127 (ttp-110) cc_final: 0.6878 (ttp-110) REVERT: D 93 LYS cc_start: 0.8568 (tptp) cc_final: 0.7984 (mmmm) REVERT: D 156 LYS cc_start: 0.8459 (mtmm) cc_final: 0.8150 (mtmt) REVERT: D 261 THR cc_start: 0.8414 (m) cc_final: 0.7926 (t) REVERT: E 178 GLU cc_start: 0.7824 (mt-10) cc_final: 0.7496 (mt-10) REVERT: E 296 MET cc_start: 0.7336 (ttp) cc_final: 0.7093 (ttp) REVERT: E 301 SER cc_start: 0.8761 (m) cc_final: 0.8369 (m) REVERT: E 305 ILE cc_start: 0.8377 (mm) cc_final: 0.8007 (mm) REVERT: E 337 ILE cc_start: 0.8650 (tp) cc_final: 0.8352 (tp) REVERT: E 356 TYR cc_start: 0.5297 (OUTLIER) cc_final: 0.4966 (t80) REVERT: I 13 MET cc_start: 0.4769 (OUTLIER) cc_final: 0.4348 (ppp) REVERT: L 60 ASP cc_start: 0.7575 (t0) cc_final: 0.7304 (t70) REVERT: L 79 GLN cc_start: 0.7516 (mp10) cc_final: 0.7226 (mp10) REVERT: K 102 ARG cc_start: 0.8609 (mmm-85) cc_final: 0.8387 (mmm-85) outliers start: 57 outliers final: 53 residues processed: 357 average time/residue: 0.3064 time to fit residues: 162.6844 Evaluate side-chains 373 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 318 time to evaluate : 2.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 85 ASN Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 211 SER Chi-restraints excluded: chain A residue 236 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 16 THR Chi-restraints excluded: chain B residue 49 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 141 MET Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 258 PHE Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 115 MET Chi-restraints excluded: chain C residue 173 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 259 LEU Chi-restraints excluded: chain D residue 13 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 88 ASN Chi-restraints excluded: chain D residue 131 MET 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 258 PHE Chi-restraints excluded: chain D residue 286 MET Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 177 GLU Chi-restraints excluded: chain E residue 188 VAL Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 209 THR Chi-restraints excluded: chain E residue 253 VAL Chi-restraints excluded: chain E residue 275 THR Chi-restraints excluded: chain E residue 356 TYR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 13 MET Chi-restraints excluded: chain I residue 74 THR Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 20 LEU Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 91 THR Chi-restraints excluded: chain L residue 11 MET Chi-restraints excluded: chain L residue 14 SER Chi-restraints excluded: chain L residue 31 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 112 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.6980 chunk 50 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 68 optimal weight: 0.3980 chunk 168 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 0.0040 chunk 144 optimal weight: 2.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 224 GLN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 HIS J 43 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.132704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.104236 restraints weight = 21189.958| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.71 r_work: 0.2880 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2734 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17835 Z= 0.194 Angle : 0.524 9.540 24256 Z= 0.264 Chirality : 0.042 0.250 2799 Planarity : 0.004 0.040 2985 Dihedral : 5.230 56.050 2822 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 3.40 % Allowed : 17.21 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.19), residues: 2103 helix: 1.62 (0.22), residues: 579 sheet: -0.39 (0.20), residues: 638 loop : -0.59 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP C 241 HIS 0.006 0.001 HIS B 142 PHE 0.021 0.001 PHE C 306 TYR 0.022 0.001 TYR A 299 ARG 0.007 0.000 ARG C 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4262.88 seconds wall clock time: 78 minutes 18.55 seconds (4698.55 seconds total)