Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 8 19:38:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3s_22031/07_2023/6x3s_22031_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3s_22031/07_2023/6x3s_22031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3s_22031/07_2023/6x3s_22031.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3s_22031/07_2023/6x3s_22031.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3s_22031/07_2023/6x3s_22031_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3s_22031/07_2023/6x3s_22031_updated.pdb" } resolution = 3.12 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 97 5.16 5 C 11245 2.51 5 N 2828 2.21 5 O 3237 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 18": "NH1" <-> "NH2" Residue "A ARG 68": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 147": "OE1" <-> "OE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A ARG 312": "NH1" <-> "NH2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 37": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 120": "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 ARG 187": "NH1" <-> "NH2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C GLU 153": "OE1" <-> "OE2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C ARG 318": "NH1" <-> "NH2" Residue "C ARG 321": "NH1" <-> "NH2" Residue "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 ARG 37": "NH1" <-> "NH2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D ARG 120": "NH1" <-> "NH2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D GLU 144": "OE1" <-> "OE2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D GLU 170": "OE1" <-> "OE2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ARG 187": "NH1" <-> "NH2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "D GLU 303": "OE1" <-> "OE2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E GLU 162": "OE1" <-> "OE2" Residue "E ARG 176": "NH1" <-> "NH2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E ARG 197": "NH1" <-> "NH2" Residue "E ARG 207": "NH1" <-> "NH2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "E PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 327": "NH1" <-> "NH2" Residue "I GLU 17": "OE1" <-> "OE2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 104": "OE1" <-> "OE2" Residue "J GLU 10": "OE1" <-> "OE2" Residue "J GLU 89": "OE1" <-> "OE2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "J ARG 102": "NH1" <-> "NH2" Residue "L GLU 27": "OE1" <-> "OE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 10": "OE1" <-> "OE2" Residue "K GLU 42": "OE1" <-> "OE2" Residue "K GLU 46": "OE1" <-> "OE2" Residue "K ARG 98": "NH1" <-> "NH2" Residue "K ARG 102": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 17407 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 chiralities: 3 Chain: "G" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen chiralities: 9 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: 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: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'J94': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Unusual residues: {'J94': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 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 chiralities: 1 Chain: "E" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Unusual residues: {'MAN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.58, per 1000 atoms: 0.49 Number of scatterers: 17407 At special positions: 0 Unit cell: (138.278, 128.282, 136.612, 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 3237 8.00 N 2828 7.00 C 11245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.04 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.03 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 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 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 404 " - " ASN A 80 " " NAG C 404 " - " ASN C 80 " " NAG D 401 " - " ASN D 111 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN E 208 " Time building additional restraints: 7.39 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 25 sheets defined 28.9% alpha, 27.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.45 Creating SS restraints... Processing helix chain 'A' and resid 9 through 20 Processing helix chain 'A' and resid 85 through 89 removed outlier: 3.865A pdb=" N ASP A 89 " --> pdb=" O ARG A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 240 removed outlier: 4.669A pdb=" N MET A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix removed outlier: 4.203A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 271 removed outlier: 3.637A pdb=" N VAL A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 305 Processing helix chain 'A' and resid 310 through 338 Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 11 through 23 removed outlier: 3.701A pdb=" N PHE B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU B 23 " --> pdb=" O LEU B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 88 through 93 removed outlier: 3.980A pdb=" N LYS B 93 " --> pdb=" O LEU B 89 " (cutoff:3.500A) 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: 4.911A pdb=" N LEU B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix removed outlier: 3.900A pdb=" N PHE B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N TRP B 246 " --> pdb=" O GLN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 275 Processing helix chain 'B' and resid 285 through 310 Processing helix chain 'B' and resid 315 through 345 removed outlier: 3.657A pdb=" N ALA B 319 " --> pdb=" O PRO B 315 " (cutoff:3.500A) removed outlier: 3.661A 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 85 through 87 No H-bonds generated for 'chain 'C' and resid 85 through 87' Processing helix chain 'C' and resid 219 through 240 removed outlier: 4.794A pdb=" N MET C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix removed outlier: 3.554A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 271 removed outlier: 3.718A pdb=" N GLU C 270 " --> pdb=" O THR C 266 " (cutoff:3.500A) 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 13 through 22 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 88 through 93 removed outlier: 3.586A pdb=" N SER D 92 " --> pdb=" O ASN D 88 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 88 through 93' Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 224 through 229 removed outlier: 4.100A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 246 removed outlier: 3.622A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N TRP D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 276 removed outlier: 3.559A pdb=" N LEU D 264 " --> pdb=" O VAL D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 310 removed outlier: 3.714A pdb=" N PHE D 289 " --> pdb=" O ALA D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 345 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: 3.550A pdb=" N VAL E 103 " --> pdb=" O SER E 100 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS E 105 " --> pdb=" O MET E 102 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 100 through 105' Processing helix chain 'E' and resid 235 through 256 removed outlier: 5.184A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix removed outlier: 3.852A pdb=" N VAL E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER E 254 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N PHE E 255 " --> pdb=" O SER E 251 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N TRP E 256 " --> pdb=" O TRP E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 286 removed outlier: 4.065A pdb=" N ILE E 282 " --> pdb=" O THR E 278 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA E 283 " --> pdb=" O LEU E 279 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG E 284 " --> pdb=" O SER E 280 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER E 286 " --> pdb=" O ILE E 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 323 removed outlier: 3.953A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 353 removed outlier: 4.074A pdb=" N LYS E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET E 331 " --> pdb=" O ARG E 327 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ASP E 332 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 4.002A 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 29 through 31 No H-bonds generated for 'chain 'J' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'A' and resid 164 through 168 removed outlier: 6.441A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 147 through 155 removed outlier: 3.838A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.695A 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: 6.896A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.879A 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: 6.205A pdb=" N THR B 39 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N GLU B 170 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL B 41 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N THR B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 4.632A 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: 4.155A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.701A 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: 6.462A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.787A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.836A 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: 6.891A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 6.769A 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: 6.202A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 45 through 47 Processing sheet with id= L, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.055A pdb=" N SER D 159 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N VAL D 211 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 179 through 183 removed outlier: 5.995A pdb=" N THR E 51 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N GLN E 182 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ILE E 53 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 111 through 113 removed outlier: 4.613A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 59 through 62 removed outlier: 6.832A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 116 through 121 removed outlier: 7.024A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 4 through 7 Processing sheet with id= R, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.212A 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: 5.958A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.669A 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: 6.117A pdb=" N LYS J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N TRP J 47 " --> pdb=" O LYS J 38 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= W, first strand: chain 'L' and resid 85 through 90 removed outlier: 6.160A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'K' and resid 3 through 6 Processing sheet with id= Y, first strand: chain 'K' and resid 57 through 60 removed outlier: 3.739A pdb=" N ASP K 57 " --> pdb=" O ASP K 52 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 745 hydrogen bonds defined for protein. 2184 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: 4.84 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: 1.21 - 1.33: 4870 1.33 - 1.45: 3507 1.45 - 1.57: 9309 1.57 - 1.69: 0 1.69 - 1.81: 167 Bond restraints: 17853 Sorted by residual: bond pdb=" C09 J94 A 405 " pdb=" O10 J94 A 405 " ideal model delta sigma weight residual 1.351 1.224 0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C09 J94 C 405 " pdb=" O10 J94 C 405 " ideal model delta sigma weight residual 1.351 1.225 0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" C25 J94 A 405 " pdb=" O24 J94 A 405 " ideal model delta sigma weight residual 1.350 1.225 0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" C25 J94 C 405 " pdb=" O24 J94 C 405 " ideal model delta sigma weight residual 1.350 1.225 0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" C13 J94 A 405 " pdb=" O12 J94 A 405 " ideal model delta sigma weight residual 1.349 1.226 0.123 2.00e-02 2.50e+03 3.78e+01 ... (remaining 17848 not shown) Histogram of bond angle deviations from ideal: 97.73 - 105.00: 332 105.00 - 112.27: 9222 112.27 - 119.55: 5393 119.55 - 126.82: 9084 126.82 - 134.09: 265 Bond angle restraints: 24296 Sorted by residual: angle pdb=" C ALA D 152 " pdb=" N CYS D 153 " pdb=" CA CYS D 153 " ideal model delta sigma weight residual 122.15 109.44 12.71 3.47e+00 8.31e-02 1.34e+01 angle pdb=" C SER E 164 " pdb=" N CYS E 165 " pdb=" CA CYS E 165 " ideal model delta sigma weight residual 122.38 111.99 10.39 2.90e+00 1.19e-01 1.28e+01 angle pdb=" CA CYS E 165 " pdb=" CB CYS E 165 " pdb=" SG CYS E 165 " ideal model delta sigma weight residual 114.40 122.37 -7.97 2.30e+00 1.89e-01 1.20e+01 angle pdb=" CA ASN E 208 " pdb=" C ASN E 208 " pdb=" O ASN E 208 " ideal model delta sigma weight residual 121.94 118.28 3.66 1.15e+00 7.56e-01 1.01e+01 angle pdb=" CA ASN B 111 " pdb=" C ASN B 111 " pdb=" O ASN B 111 " ideal model delta sigma weight residual 121.78 118.36 3.42 1.12e+00 7.97e-01 9.31e+00 ... (remaining 24291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.15: 9881 25.15 - 50.30: 432 50.30 - 75.44: 37 75.44 - 100.59: 11 100.59 - 125.74: 2 Dihedral angle restraints: 10363 sinusoidal: 4107 harmonic: 6256 Sorted by residual: dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 165 " pdb=" CB CYS E 165 " ideal model delta sinusoidal sigma weight residual -86.00 -21.06 -64.94 1 1.00e+01 1.00e-02 5.53e+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 -155.08 -24.92 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA VAL D 64 " pdb=" C VAL D 64 " pdb=" N PHE D 65 " pdb=" CA PHE D 65 " ideal model delta harmonic sigma weight residual 180.00 157.27 22.73 0 5.00e+00 4.00e-02 2.07e+01 ... (remaining 10360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 2785 0.159 - 0.319: 11 0.319 - 0.478: 0 0.478 - 0.637: 1 0.637 - 0.797: 3 Chirality restraints: 2800 Sorted by residual: chirality pdb=" C1 MAN G 9 " pdb=" O2 MAN G 8 " pdb=" C2 MAN G 9 " pdb=" O5 MAN G 9 " both_signs ideal model delta sigma weight residual False 2.40 1.60 0.80 2.00e-02 2.50e+03 1.59e+03 chirality pdb=" C1 MAN G 7 " pdb=" O6 BMA G 3 " pdb=" C2 MAN G 7 " pdb=" O5 MAN G 7 " both_signs ideal model delta sigma weight residual False 2.40 1.64 0.76 2.00e-02 2.50e+03 1.43e+03 chirality pdb=" C1 MAN G 5 " pdb=" O2 MAN G 4 " pdb=" C2 MAN G 5 " pdb=" O5 MAN G 5 " both_signs ideal model delta sigma weight residual False 2.40 1.70 0.70 2.00e-02 2.50e+03 1.21e+03 ... (remaining 2797 not shown) Planarity restraints: 2992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG H 2 " 0.144 2.00e-02 2.50e+03 1.18e-01 1.74e+02 pdb=" C7 NAG H 2 " -0.039 2.00e-02 2.50e+03 pdb=" C8 NAG H 2 " 0.107 2.00e-02 2.50e+03 pdb=" N2 NAG H 2 " -0.187 2.00e-02 2.50e+03 pdb=" O7 NAG H 2 " -0.025 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 1.42e+02 pdb=" C7 NAG G 2 " 0.035 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " -0.096 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " 0.171 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " -0.102 2.00e-02 2.50e+03 8.38e-02 8.79e+01 pdb=" C7 NAG M 2 " 0.028 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " -0.077 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " 0.133 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " 0.017 2.00e-02 2.50e+03 ... (remaining 2989 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 346 2.68 - 3.23: 16229 3.23 - 3.79: 27089 3.79 - 4.34: 37638 4.34 - 4.90: 63243 Nonbonded interactions: 144545 Sorted by model distance: nonbonded pdb=" O SER B 241 " pdb=" OG SER B 244 " model vdw 2.119 2.440 nonbonded pdb=" O VAL D 307 " pdb=" OG1 THR D 311 " model vdw 2.128 2.440 nonbonded pdb=" OH TYR B 26 " pdb=" OD2 ASP B 72 " model vdw 2.193 2.440 nonbonded pdb=" OG1 THR D 99 " pdb=" OH TYR D 169 " model vdw 2.227 2.440 nonbonded pdb=" OG SER I 7 " pdb=" OG SER I 22 " model vdw 2.260 2.440 ... (remaining 144540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 10 through 347) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 1 through 105) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 2 through 117) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.800 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: 6.510 Check model and map are aligned: 0.250 Set scattering table: 0.130 Process input model: 43.980 Find NCS groups from input model: 0.930 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 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 0.127 17853 Z= 0.366 Angle : 0.656 12.708 24296 Z= 0.337 Chirality : 0.053 0.797 2800 Planarity : 0.005 0.118 2985 Dihedral : 13.752 125.739 6316 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer Outliers : 0.05 % 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: -2.03 (0.16), residues: 2103 helix: -0.08 (0.20), residues: 584 sheet: -1.41 (0.18), residues: 654 loop : -2.08 (0.18), residues: 865 *********************** 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 431 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 430 time to evaluate : 2.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 431 average time/residue: 0.3440 time to fit residues: 213.5132 Evaluate side-chains 355 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 2.003 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.8455 ------------------------------------------------------------------------------- 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: 0.3980 chunk 156 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 83 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 98 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 90 GLN A 113 ASN A 303 ASN A 309 GLN B 68 GLN B 110 HIS B 116 ASN B 190 GLN ** B 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN C 265 ASN C 309 GLN D 68 GLN D 88 ASN D 116 ASN D 275 ASN D 308 ASN E 33 ASN E 80 GLN E 128 ASN E 135 ASN ** E 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 347 ASN I 37 GLN I 53 ASN ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 6 GLN J 55 ASN ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN L 38 GLN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 6 GLN K 39 GLN K 77 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 17853 Z= 0.213 Angle : 0.553 11.939 24296 Z= 0.274 Chirality : 0.042 0.172 2800 Planarity : 0.004 0.063 2985 Dihedral : 6.109 120.467 2376 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 1.65 % 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: -1.10 (0.17), residues: 2103 helix: 0.96 (0.21), residues: 583 sheet: -1.02 (0.19), residues: 654 loop : -1.60 (0.19), residues: 866 *********************** 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 393 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 362 time to evaluate : 2.053 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 22 residues processed: 374 average time/residue: 0.3033 time to fit residues: 170.4043 Evaluate side-chains 368 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 346 time to evaluate : 2.076 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.1653 time to fit residues: 9.4293 ------------------------------------------------------------------------------- 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: 4.9990 chunk 58 optimal weight: 6.9990 chunk 156 optimal weight: 0.8980 chunk 128 optimal weight: 1.9990 chunk 51 optimal weight: 4.9990 chunk 188 optimal weight: 0.9990 chunk 203 optimal weight: 2.9990 chunk 167 optimal weight: 4.9990 chunk 186 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 151 optimal weight: 6.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN B 242 GLN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 ASN E 156 HIS ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.031 17853 Z= 0.309 Angle : 0.580 12.768 24296 Z= 0.289 Chirality : 0.044 0.171 2800 Planarity : 0.004 0.066 2985 Dihedral : 6.321 124.016 2376 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % 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: -0.71 (0.18), residues: 2103 helix: 1.31 (0.21), residues: 586 sheet: -0.86 (0.19), residues: 657 loop : -1.34 (0.20), residues: 860 *********************** 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 379 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 356 time to evaluate : 2.082 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 368 average time/residue: 0.2991 time to fit residues: 164.5298 Evaluate side-chains 352 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 340 time to evaluate : 2.024 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.2192 time to fit residues: 6.9698 ------------------------------------------------------------------------------- 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: 9.9990 chunk 141 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 200 optimal weight: 7.9990 chunk 98 optimal weight: 0.7980 chunk 179 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 332 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 110 HIS E 135 ASN ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 17853 Z= 0.344 Angle : 0.599 12.818 24296 Z= 0.299 Chirality : 0.044 0.174 2800 Planarity : 0.004 0.069 2985 Dihedral : 6.398 123.763 2376 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.18), residues: 2103 helix: 1.42 (0.21), residues: 586 sheet: -0.77 (0.19), residues: 658 loop : -1.20 (0.20), residues: 859 *********************** 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 397 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 353 time to evaluate : 2.220 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 28 residues processed: 378 average time/residue: 0.3110 time to fit residues: 176.6450 Evaluate side-chains 362 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 334 time to evaluate : 2.008 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1778 time to fit residues: 11.6719 ------------------------------------------------------------------------------- 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: 6.9990 chunk 113 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 148 optimal weight: 0.0030 chunk 82 optimal weight: 2.9990 chunk 170 optimal weight: 8.9990 chunk 138 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 179 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 overall best weight: 2.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 332 ASN ** C 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 HIS E 33 ASN E 135 ASN ** J 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 17853 Z= 0.264 Angle : 0.570 12.265 24296 Z= 0.284 Chirality : 0.043 0.166 2800 Planarity : 0.004 0.068 2985 Dihedral : 6.315 122.970 2376 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer Outliers : 1.59 % 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: -0.35 (0.18), residues: 2103 helix: 1.57 (0.21), residues: 587 sheet: -0.66 (0.20), residues: 648 loop : -1.07 (0.21), residues: 868 *********************** 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 380 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 350 time to evaluate : 1.937 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 13 residues processed: 366 average time/residue: 0.3377 time to fit residues: 186.5879 Evaluate side-chains 355 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 342 time to evaluate : 2.350 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.2957 time to fit residues: 8.9752 ------------------------------------------------------------------------------- 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: 0.9980 chunk 180 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 117 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 200 optimal weight: 7.9990 chunk 166 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 105 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 ASN E 33 ASN E 135 ASN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN J 110 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 17853 Z= 0.170 Angle : 0.535 10.973 24296 Z= 0.266 Chirality : 0.042 0.155 2800 Planarity : 0.004 0.069 2985 Dihedral : 6.156 122.648 2376 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 1.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.18), residues: 2103 helix: 1.73 (0.22), residues: 583 sheet: -0.51 (0.20), residues: 645 loop : -0.92 (0.21), residues: 875 *********************** 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 390 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 358 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 18 residues processed: 371 average time/residue: 0.2912 time to fit residues: 162.2354 Evaluate side-chains 352 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 334 time to evaluate : 1.828 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1621 time to fit residues: 7.7967 ------------------------------------------------------------------------------- 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: 10.0000 chunk 22 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 146 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 111 optimal weight: 4.9990 chunk 199 optimal weight: 6.9990 chunk 124 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN A 224 GLN ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 ASN E 33 ASN E 135 ASN E 154 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 17853 Z= 0.374 Angle : 0.617 12.769 24296 Z= 0.308 Chirality : 0.045 0.182 2800 Planarity : 0.005 0.074 2985 Dihedral : 6.432 124.402 2376 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer Outliers : 1.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.18), residues: 2103 helix: 1.61 (0.22), residues: 587 sheet: -0.62 (0.20), residues: 655 loop : -0.94 (0.21), residues: 861 *********************** 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 370 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 341 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 20 residues processed: 358 average time/residue: 0.3116 time to fit residues: 166.7079 Evaluate side-chains 353 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 333 time to evaluate : 2.129 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1982 time to fit residues: 9.6547 ------------------------------------------------------------------------------- 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: 5.9990 chunk 79 optimal weight: 0.4980 chunk 119 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 126 optimal weight: 1.9990 chunk 135 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 ASN E 33 ASN E 135 ASN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 17853 Z= 0.214 Angle : 0.559 11.871 24296 Z= 0.278 Chirality : 0.043 0.173 2800 Planarity : 0.004 0.076 2985 Dihedral : 6.259 122.787 2376 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % 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: -0.10 (0.18), residues: 2103 helix: 1.73 (0.22), residues: 586 sheet: -0.53 (0.20), residues: 652 loop : -0.88 (0.21), residues: 865 *********************** 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 364 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 350 time to evaluate : 2.005 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 6 residues processed: 356 average time/residue: 0.3127 time to fit residues: 166.6590 Evaluate side-chains 337 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 331 time to evaluate : 1.826 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1649 time to fit residues: 4.3800 ------------------------------------------------------------------------------- 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: 0.8980 chunk 191 optimal weight: 0.6980 chunk 174 optimal weight: 2.9990 chunk 185 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 175 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 54 ASN ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 33 ASN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN J 110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 17853 Z= 0.221 Angle : 0.567 11.554 24296 Z= 0.280 Chirality : 0.043 0.171 2800 Planarity : 0.004 0.076 2985 Dihedral : 6.246 122.839 2376 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer Outliers : 0.42 % 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: -0.05 (0.18), residues: 2103 helix: 1.74 (0.22), residues: 586 sheet: -0.48 (0.20), residues: 652 loop : -0.84 (0.21), residues: 865 *********************** 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 345 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 337 time to evaluate : 1.989 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 339 average time/residue: 0.3434 time to fit residues: 174.5304 Evaluate side-chains 337 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 332 time to evaluate : 1.832 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1614 time to fit residues: 3.9844 ------------------------------------------------------------------------------- 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: 8.9990 chunk 119 optimal weight: 5.9990 chunk 93 optimal weight: 0.9980 chunk 136 optimal weight: 1.9990 chunk 206 optimal weight: 2.9990 chunk 189 optimal weight: 0.9990 chunk 164 optimal weight: 2.9990 chunk 17 optimal weight: 0.0370 chunk 126 optimal weight: 7.9990 chunk 100 optimal weight: 0.3980 chunk 130 optimal weight: 1.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN E 33 ASN ** E 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 17853 Z= 0.162 Angle : 0.542 11.592 24296 Z= 0.268 Chirality : 0.042 0.161 2800 Planarity : 0.004 0.077 2985 Dihedral : 6.125 122.500 2376 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer Outliers : 0.42 % 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: 0.08 (0.18), residues: 2103 helix: 1.81 (0.21), residues: 588 sheet: -0.31 (0.20), residues: 640 loop : -0.82 (0.21), residues: 875 ********************** 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 354 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 346 time to evaluate : 2.008 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 348 average time/residue: 0.3073 time to fit residues: 160.3954 Evaluate side-chains 340 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 336 time to evaluate : 1.981 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1773 time to fit residues: 3.9302 ------------------------------------------------------------------------------- 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: 0.1980 chunk 50 optimal weight: 0.8980 chunk 151 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 164 optimal weight: 0.4980 chunk 68 optimal weight: 0.5980 chunk 168 optimal weight: 4.9990 chunk 20 optimal weight: 0.2980 chunk 30 optimal weight: 0.0170 chunk 144 optimal weight: 0.6980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 41 ASN ** C 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN E 33 ASN L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.132753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.105905 restraints weight = 25804.325| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.08 r_work: 0.3117 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 17853 Z= 0.131 Angle : 0.533 11.538 24296 Z= 0.263 Chirality : 0.041 0.172 2800 Planarity : 0.004 0.076 2985 Dihedral : 5.982 121.941 2376 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer Outliers : 0.16 % 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: 0.21 (0.19), residues: 2103 helix: 1.85 (0.21), residues: 588 sheet: -0.16 (0.20), residues: 640 loop : -0.75 (0.21), residues: 875 =============================================================================== Job complete usr+sys time: 4143.94 seconds wall clock time: 76 minutes 6.49 seconds (4566.49 seconds total)