Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 8 19:53:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3v_22034/07_2023/6x3v_22034_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3v_22034/07_2023/6x3v_22034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3v_22034/07_2023/6x3v_22034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3v_22034/07_2023/6x3v_22034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3v_22034/07_2023/6x3v_22034_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3v_22034/07_2023/6x3v_22034_updated.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 11253 2.51 5 N 2833 2.21 5 O 3243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 17": "OD1" <-> "OD2" Residue "A ASP 30": "OD1" <-> "OD2" Residue "A ASP 43": "OD1" <-> "OD2" Residue "A ASP 48": "OD1" <-> "OD2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A ASP 162": "OD1" <-> "OD2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A ASP 245": "OD1" <-> "OD2" 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 ASP 27": "OD1" <-> "OD2" Residue "B GLU 36": "OE1" <-> "OE2" Residue "B ASP 55": "OD1" <-> "OD2" 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 ASP 145": "OD1" <-> "OD2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "B ARG 274": "NH1" <-> "NH2" Residue "B PHE 298": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C ASP 17": "OD1" <-> "OD2" 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 ASP 172": "OD1" <-> "OD2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "C PHE 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C ARG 318": "NH1" <-> "NH2" Residue "C ARG 321": "NH1" <-> "NH2" Residue "C TYR 335": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 17": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D GLU 36": "OE1" <-> "OE2" Residue "D ASP 55": "OD1" <-> "OD2" Residue "D ASP 63": "OD1" <-> "OD2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D ASP 184": "OD1" <-> "OD2" Residue "D ARG 187": "NH1" <-> "NH2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ASP 287": "OD1" <-> "OD2" Residue "E GLU 36": "OE1" <-> "OE2" Residue "E ARG 85": "NH1" <-> "NH2" 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 PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 176": "NH1" <-> "NH2" Residue "E ARG 185": "NH1" <-> "NH2" Residue "E GLU 189": "OE1" <-> "OE2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E ARG 197": "NH1" <-> "NH2" Residue "E ARG 207": "NH1" <-> "NH2" Residue "E ARG 327": "NH1" <-> "NH2" Residue "I GLU 17": "OE1" <-> "OE2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I GLU 41": "OE1" <-> "OE2" Residue "I ASP 70": "OD1" <-> "OD2" Residue "I PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "I GLU 104": "OE1" <-> "OE2" Residue "J GLU 46": "OE1" <-> "OE2" Residue "J ASP 57": "OD1" <-> "OD2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "J ARG 102": "NH1" <-> "NH2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L GLU 104": "OE1" <-> "OE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K GLU 89": "OE1" <-> "OE2" Residue "K ASP 90": "OD1" <-> "OD2" Residue "K ARG 98": "NH1" <-> "NH2" Residue "K ARG 102": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 17426 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2729 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen 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 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 chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'ABU': 1, 'NAG': 1, 'V8D': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'ABU': 1, 'NAG': 1, 'V8D': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.54, per 1000 atoms: 0.49 Number of scatterers: 17426 At special positions: 0 Unit cell: (135.779, 121.618, 129.948, 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 3243 8.00 N 2833 7.00 C 11253 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.03 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " " MAN G 8 " - " MAN G 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 10 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG A 404 " - " ASN A 80 " " NAG C 404 " - " ASN C 80 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN D 111 " " NAG N 1 " - " ASN E 208 " Time building additional restraints: 7.38 Conformation dependent library (CDL) restraints added in 2.5 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: 36 helices and 28 sheets defined 27.9% alpha, 24.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 8 through 20 Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 219 through 225 Processing helix chain 'A' and resid 227 through 240 removed outlier: 4.052A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 269 removed outlier: 3.974A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 304 Processing helix chain 'A' and resid 310 through 339 removed outlier: 4.039A pdb=" N ALA A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 11 through 22 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 224 through 245 removed outlier: 3.526A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix removed outlier: 4.034A pdb=" N SER B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 275 removed outlier: 3.742A pdb=" N ARG B 274 " --> pdb=" O SER B 270 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN B 275 " --> pdb=" O ILE B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 310 Processing helix chain 'B' and resid 315 through 345 removed outlier: 3.938A 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 8 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 224 Processing helix chain 'C' and resid 226 through 240 removed outlier: 3.613A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 269 Processing helix chain 'C' and resid 280 through 304 Processing helix chain 'C' and resid 310 through 338 Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 11 through 23 Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' 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 245 removed outlier: 4.319A pdb=" N LEU D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Proline residue: D 233 - end of helix removed outlier: 4.156A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 275 Processing helix chain 'D' and resid 285 through 310 Processing helix chain 'D' and resid 315 through 345 removed outlier: 4.151A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N PHE D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Proline residue: D 330 - end of helix Processing helix chain 'E' and resid 27 through 34 Processing helix chain 'E' and resid 235 through 255 removed outlier: 5.178A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix removed outlier: 4.248A pdb=" N SER E 254 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N PHE E 255 " --> pdb=" O SER E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 286 Processing helix chain 'E' and resid 296 through 323 removed outlier: 3.856A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 355 removed outlier: 3.755A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 3.668A 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 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing sheet with id= A, first strand: chain 'A' and resid 164 through 168 removed outlier: 6.508A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 43 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 64 through 68 Processing sheet with id= C, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.845A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 167 through 171 removed outlier: 6.253A pdb=" N THR B 39 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N GLU B 170 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL B 41 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 179 through 181 removed outlier: 6.484A pdb=" N ILE B 45 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 99 through 101 Processing sheet with id= G, first strand: chain 'B' and resid 150 through 154 removed outlier: 3.781A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LEU B 193 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.452A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.562A pdb=" N LEU C 210 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 39 through 43 Processing sheet with id= K, first strand: chain 'D' and resid 179 through 181 removed outlier: 6.607A pdb=" N ILE D 45 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR D 130 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) 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 152 through 154 removed outlier: 3.812A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 179 through 183 removed outlier: 5.794A pdb=" N THR E 51 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLN E 182 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE E 53 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.541A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 116 through 121 removed outlier: 7.089A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 4 through 7 Processing sheet with id= R, first strand: chain 'I' and resid 10 through 12 removed outlier: 5.768A pdb=" N LYS I 102 " --> pdb=" O MET I 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'I' and resid 85 through 90 removed outlier: 6.177A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'J' and resid 3 through 6 Processing sheet with id= U, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.703A pdb=" N TRP J 36 " --> pdb=" O GLY J 49 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N LYS J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N TRP J 47 " --> pdb=" O LYS J 38 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 17 through 19 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: 6.319A pdb=" N LYS L 102 " --> pdb=" O MET L 11 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N MET L 13 " --> pdb=" O LYS L 102 " (cutoff:3.500A) removed outlier: 5.931A 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: 6.094A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 3 through 6 removed outlier: 3.596A pdb=" N VAL K 18 " --> pdb=" O LEU K 83 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'K' and resid 10 through 12 Processing sheet with id= AB, first strand: chain 'K' and resid 57 through 60 removed outlier: 3.813A pdb=" N ASP K 57 " --> pdb=" O ASP K 52 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N TYR K 33 " --> pdb=" O LYS K 99 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS K 99 " --> pdb=" O TYR K 33 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 697 hydrogen bonds defined for protein. 2031 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: 4.96 Time building geometry restraints manager: 7.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2670 1.31 - 1.43: 5257 1.43 - 1.56: 9767 1.56 - 1.69: 1 1.69 - 1.82: 167 Bond restraints: 17862 Sorted by residual: bond pdb=" C13 V8D A 406 " pdb=" O02 V8D A 406 " ideal model delta sigma weight residual 1.209 1.398 -0.189 2.00e-02 2.50e+03 8.94e+01 bond pdb=" C13 V8D C 406 " pdb=" O02 V8D C 406 " ideal model delta sigma weight residual 1.209 1.397 -0.188 2.00e-02 2.50e+03 8.86e+01 bond pdb=" C13 V8D C 406 " pdb=" O01 V8D C 406 " ideal model delta sigma weight residual 1.325 1.180 0.145 2.00e-02 2.50e+03 5.27e+01 bond pdb=" C13 V8D A 406 " pdb=" O01 V8D A 406 " ideal model delta sigma weight residual 1.325 1.182 0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" C08 V8D C 406 " pdb=" C13 V8D C 406 " ideal model delta sigma weight residual 1.459 1.530 -0.071 2.00e-02 2.50e+03 1.25e+01 ... (remaining 17857 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.18: 442 106.18 - 113.16: 9826 113.16 - 120.13: 6255 120.13 - 127.11: 7566 127.11 - 134.09: 199 Bond angle restraints: 24288 Sorted by residual: angle pdb=" C08 V8D A 406 " pdb=" C13 V8D A 406 " pdb=" O01 V8D A 406 " ideal model delta sigma weight residual 110.46 120.42 -9.96 3.00e+00 1.11e-01 1.10e+01 angle pdb=" N GLY K 56 " pdb=" CA GLY K 56 " pdb=" C GLY K 56 " ideal model delta sigma weight residual 115.63 110.77 4.86 1.49e+00 4.50e-01 1.07e+01 angle pdb=" C08 V8D C 406 " pdb=" C13 V8D C 406 " pdb=" O01 V8D C 406 " ideal model delta sigma weight residual 110.46 120.24 -9.78 3.00e+00 1.11e-01 1.06e+01 angle pdb=" N MET B 114 " pdb=" CA MET B 114 " pdb=" C MET B 114 " ideal model delta sigma weight residual 110.13 106.39 3.74 1.15e+00 7.56e-01 1.06e+01 angle pdb=" N ALA B 161 " pdb=" CA ALA B 161 " pdb=" CB ALA B 161 " ideal model delta sigma weight residual 114.17 110.83 3.34 1.14e+00 7.69e-01 8.56e+00 ... (remaining 24283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 9331 17.85 - 35.70: 868 35.70 - 53.55: 123 53.55 - 71.40: 23 71.40 - 89.25: 6 Dihedral angle restraints: 10351 sinusoidal: 4095 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 -24.88 -61.12 1 1.00e+01 1.00e-02 4.96e+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 -31.80 -54.20 1 1.00e+01 1.00e-02 3.98e+01 dihedral pdb=" CA CYS A 150 " pdb=" C CYS A 150 " pdb=" N THR A 151 " pdb=" CA THR A 151 " ideal model delta harmonic sigma weight residual -180.00 -152.15 -27.85 0 5.00e+00 4.00e-02 3.10e+01 ... (remaining 10348 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2372 0.060 - 0.121: 406 0.121 - 0.181: 24 0.181 - 0.241: 4 0.241 - 0.302: 3 Chirality restraints: 2809 Sorted by residual: chirality pdb=" C1 NAG M 1 " pdb=" ND2 ASN D 111 " pdb=" C2 NAG M 1 " pdb=" O5 NAG M 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.10 -0.30 2.00e-01 2.50e+01 2.27e+00 chirality pdb=" C1 BMA M 3 " pdb=" O4 NAG M 2 " pdb=" C2 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 1.98e+00 chirality pdb=" C5 BMA F 3 " pdb=" C4 BMA F 3 " pdb=" C6 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 2806 not shown) Planarity restraints: 2995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL D 227 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.50e+00 pdb=" C VAL D 227 " 0.047 2.00e-02 2.50e+03 pdb=" O VAL D 227 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE D 228 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 227 " -0.009 2.00e-02 2.50e+03 1.87e-02 3.51e+00 pdb=" C VAL B 227 " 0.032 2.00e-02 2.50e+03 pdb=" O VAL B 227 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE B 228 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 277 " -0.027 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO D 278 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO D 278 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 278 " -0.022 5.00e-02 4.00e+02 ... (remaining 2992 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 420 2.69 - 3.24: 16530 3.24 - 3.79: 26621 3.79 - 4.35: 36272 4.35 - 4.90: 61918 Nonbonded interactions: 141761 Sorted by model distance: nonbonded pdb=" OG1 THR B 99 " pdb=" OH TYR B 169 " model vdw 2.136 2.440 nonbonded pdb=" OG1 THR E 111 " pdb=" OH TYR E 181 " model vdw 2.144 2.440 nonbonded pdb=" NE2 HIS C 107 " pdb=" OG1 THR C 131 " model vdw 2.194 2.520 nonbonded pdb=" OG1 THR D 99 " pdb=" OH TYR D 169 " model vdw 2.209 2.440 nonbonded pdb=" OG1 THR L 63 " pdb=" OG1 THR L 74 " model vdw 2.213 2.440 ... (remaining 141756 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 1 through 105) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 2 through 117) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.220 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: 6.490 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 44.590 Find NCS groups from input model: 0.980 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 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 : 0.006 0.189 17862 Z= 0.372 Angle : 0.653 9.958 24288 Z= 0.340 Chirality : 0.046 0.302 2809 Planarity : 0.004 0.040 2988 Dihedral : 13.521 89.249 6304 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer Outliers : 0.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.16), residues: 2103 helix: 0.10 (0.19), residues: 564 sheet: -2.64 (0.17), residues: 675 loop : -2.46 (0.18), residues: 864 *********************** 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 295 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 284 time to evaluate : 2.043 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 295 average time/residue: 0.3519 time to fit residues: 147.9163 Evaluate side-chains 247 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 240 time to evaluate : 1.850 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1506 time to fit residues: 4.6198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 87 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 162 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 187 optimal weight: 20.0000 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 90 GLN B 102 HIS B 275 ASN C 173 ASN E 80 GLN E 90 ASN E 324 GLN E 347 ASN J 82 GLN K 5 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.0685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 17862 Z= 0.217 Angle : 0.522 7.073 24288 Z= 0.267 Chirality : 0.043 0.178 2809 Planarity : 0.004 0.041 2988 Dihedral : 4.608 53.956 2364 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 2.44 % 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: -1.74 (0.18), residues: 2103 helix: 1.42 (0.21), residues: 561 sheet: -2.21 (0.18), residues: 658 loop : -1.93 (0.19), residues: 884 *********************** 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 289 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 243 time to evaluate : 2.085 Fit side-chains outliers start: 46 outliers final: 36 residues processed: 270 average time/residue: 0.3425 time to fit residues: 135.2572 Evaluate side-chains 266 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 230 time to evaluate : 1.961 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.1760 time to fit residues: 14.0751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 104 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 128 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 188 optimal weight: 6.9990 chunk 203 optimal weight: 9.9990 chunk 167 optimal weight: 3.9990 chunk 186 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 151 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 142 HIS B 275 ASN C 265 ASN C 267 HIS I 37 GLN J 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.038 17862 Z= 0.338 Angle : 0.573 10.817 24288 Z= 0.291 Chirality : 0.045 0.205 2809 Planarity : 0.004 0.040 2988 Dihedral : 4.705 56.925 2364 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 2.18 % 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: -1.38 (0.18), residues: 2103 helix: 1.68 (0.21), residues: 563 sheet: -2.01 (0.18), residues: 674 loop : -1.66 (0.20), residues: 866 *********************** 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 297 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 256 time to evaluate : 1.978 Fit side-chains revert: symmetry clash outliers start: 41 outliers final: 27 residues processed: 287 average time/residue: 0.3170 time to fit residues: 135.4699 Evaluate side-chains 266 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 239 time to evaluate : 2.186 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 0 residues processed: 27 average time/residue: 0.1623 time to fit residues: 11.0927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 186 optimal weight: 0.9980 chunk 141 optimal weight: 5.9990 chunk 97 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 200 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 179 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 265 ASN I 6 GLN K 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 17862 Z= 0.211 Angle : 0.524 9.339 24288 Z= 0.264 Chirality : 0.042 0.212 2809 Planarity : 0.003 0.040 2988 Dihedral : 4.597 59.611 2364 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.18), residues: 2103 helix: 2.03 (0.21), residues: 561 sheet: -1.78 (0.19), residues: 666 loop : -1.41 (0.21), residues: 876 *********************** 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 286 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 249 time to evaluate : 2.184 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 23 residues processed: 270 average time/residue: 0.3319 time to fit residues: 132.6797 Evaluate side-chains 264 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 241 time to evaluate : 1.995 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1633 time to fit residues: 9.8098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 166 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 82 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 179 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.056 17862 Z= 0.435 Angle : 0.620 9.954 24288 Z= 0.315 Chirality : 0.046 0.250 2809 Planarity : 0.004 0.040 2988 Dihedral : 4.854 57.501 2364 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.18), residues: 2103 helix: 1.82 (0.21), residues: 563 sheet: -1.77 (0.19), residues: 664 loop : -1.50 (0.20), residues: 876 *********************** 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 299 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 262 time to evaluate : 1.998 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 24 residues processed: 286 average time/residue: 0.3105 time to fit residues: 133.0610 Evaluate side-chains 277 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 253 time to evaluate : 2.026 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.1821 time to fit residues: 10.5902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 67 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 200 optimal weight: 8.9990 chunk 166 optimal weight: 0.0980 chunk 92 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 105 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 242 GLN C 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 17862 Z= 0.153 Angle : 0.512 8.405 24288 Z= 0.257 Chirality : 0.042 0.209 2809 Planarity : 0.003 0.039 2988 Dihedral : 4.523 57.981 2364 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer Outliers : 1.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.19), residues: 2103 helix: 2.30 (0.21), residues: 558 sheet: -1.58 (0.19), residues: 672 loop : -1.22 (0.21), residues: 873 *********************** 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 278 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 255 time to evaluate : 2.039 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 264 average time/residue: 0.3249 time to fit residues: 127.5053 Evaluate side-chains 261 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 247 time to evaluate : 1.900 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1659 time to fit residues: 7.1211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 193 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 114 optimal weight: 0.7980 chunk 146 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 168 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 199 optimal weight: 3.9990 chunk 124 optimal weight: 0.9990 chunk 121 optimal weight: 0.0870 chunk 92 optimal weight: 5.9990 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.042 17862 Z= 0.155 Angle : 0.516 8.486 24288 Z= 0.257 Chirality : 0.042 0.206 2809 Planarity : 0.003 0.042 2988 Dihedral : 4.340 57.741 2364 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.74 % 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: -0.43 (0.19), residues: 2103 helix: 2.48 (0.21), residues: 560 sheet: -1.45 (0.19), residues: 683 loop : -1.07 (0.21), residues: 860 *********************** 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 267 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 253 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 259 average time/residue: 0.3457 time to fit residues: 132.2236 Evaluate side-chains 255 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 247 time to evaluate : 1.768 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1735 time to fit residues: 5.1587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 123 optimal weight: 0.9990 chunk 79 optimal weight: 0.4980 chunk 119 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 156 optimal weight: 8.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 17862 Z= 0.205 Angle : 0.531 8.276 24288 Z= 0.265 Chirality : 0.043 0.214 2809 Planarity : 0.003 0.040 2988 Dihedral : 4.314 54.770 2364 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.19), residues: 2103 helix: 2.47 (0.21), residues: 560 sheet: -1.41 (0.19), residues: 685 loop : -1.05 (0.22), residues: 858 *********************** 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 259 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 243 time to evaluate : 1.940 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 9 residues processed: 250 average time/residue: 0.3321 time to fit residues: 123.5150 Evaluate side-chains 251 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 242 time to evaluate : 2.036 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1804 time to fit residues: 5.8293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 181 optimal weight: 7.9990 chunk 191 optimal weight: 0.7980 chunk 174 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 80 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN C 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 17862 Z= 0.257 Angle : 0.555 8.382 24288 Z= 0.276 Chirality : 0.044 0.239 2809 Planarity : 0.003 0.040 2988 Dihedral : 4.409 54.631 2364 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 0.48 % 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: -0.47 (0.19), residues: 2103 helix: 2.39 (0.21), residues: 561 sheet: -1.47 (0.19), residues: 691 loop : -1.04 (0.22), residues: 851 *********************** 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 248 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 239 time to evaluate : 1.969 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 242 average time/residue: 0.3323 time to fit residues: 118.7352 Evaluate side-chains 244 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 240 time to evaluate : 1.820 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1682 time to fit residues: 4.0153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 196 optimal weight: 0.0470 chunk 119 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 206 optimal weight: 0.9990 chunk 189 optimal weight: 4.9990 chunk 164 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 overall best weight: 1.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN C 265 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 17862 Z= 0.247 Angle : 0.555 8.288 24288 Z= 0.276 Chirality : 0.043 0.227 2809 Planarity : 0.003 0.040 2988 Dihedral : 4.399 51.612 2364 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.19), residues: 2103 helix: 2.39 (0.21), residues: 561 sheet: -1.47 (0.19), residues: 691 loop : -1.01 (0.22), residues: 851 ********************** 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 250 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 245 time to evaluate : 1.891 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 247 average time/residue: 0.3290 time to fit residues: 121.2669 Evaluate side-chains 247 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 243 time to evaluate : 2.321 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1690 time to fit residues: 4.0406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 207 random chunks: chunk 174 optimal weight: 0.0050 chunk 50 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 24 optimal weight: 0.0670 chunk 45 optimal weight: 0.9980 chunk 164 optimal weight: 0.9980 chunk 68 optimal weight: 0.4980 chunk 168 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.4932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** B 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.133428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.106189 restraints weight = 21183.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.109325 restraints weight = 12637.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.111342 restraints weight = 9133.559| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.064 17862 Z= 0.143 Angle : 0.523 7.733 24288 Z= 0.260 Chirality : 0.042 0.218 2809 Planarity : 0.003 0.042 2988 Dihedral : 4.254 55.380 2364 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer Outliers : 0.32 % 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: -0.24 (0.19), residues: 2103 helix: 2.59 (0.21), residues: 562 sheet: -1.36 (0.19), residues: 693 loop : -0.89 (0.22), residues: 848 =============================================================================== Job complete usr+sys time: 3353.26 seconds wall clock time: 62 minutes 21.46 seconds (3741.46 seconds total)