Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 11:30:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3w_22035/04_2023/6x3w_22035_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3w_22035/04_2023/6x3w_22035.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3w_22035/04_2023/6x3w_22035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3w_22035/04_2023/6x3w_22035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3w_22035/04_2023/6x3w_22035_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6x3w_22035/04_2023/6x3w_22035_updated.pdb" } resolution = 3.3 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 11235 2.51 5 N 2832 2.21 5 O 3235 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 14": "OE1" <-> "OE2" Residue "A ARG 18": "NH1" <-> "NH2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 142": "NH1" <-> "NH2" Residue "A GLU 165": "OE1" <-> "OE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A ARG 318": "NH1" <-> "NH2" Residue "A ARG 321": "NH1" <-> "NH2" Residue "B ARG 17": "NH1" <-> "NH2" Residue "B ARG 21": "NH1" <-> "NH2" Residue "B ARG 67": "NH1" <-> "NH2" Residue "B ARG 85": "NH1" <-> "NH2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B ARG 136": "NH1" <-> "NH2" Residue "B GLU 144": "OE1" <-> "OE2" Residue "B ARG 164": "NH1" <-> "NH2" Residue "B GLU 170": "OE1" <-> "OE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B ARG 187": "NH1" <-> "NH2" Residue "C GLU 14": "OE1" <-> "OE2" Residue "C ARG 18": "NH1" <-> "NH2" Residue "C GLU 52": "OE1" <-> "OE2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C ARG 142": "NH1" <-> "NH2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C ARG 318": "NH1" <-> "NH2" Residue "C ARG 321": "NH1" <-> "NH2" Residue "D ARG 17": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D GLU 40": "OE1" <-> "OE2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D ARG 136": "NH1" <-> "NH2" Residue "D GLU 138": "OE1" <-> "OE2" Residue "D PHE 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 164": "NH1" <-> "NH2" Residue "D ARG 173": "NH1" <-> "NH2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D ARG 249": "NH1" <-> "NH2" Residue "D GLU 250": "OE1" <-> "OE2" Residue "E ARG 97": "NH1" <-> "NH2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E ARG 144": "NH1" <-> "NH2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E GLU 168": "OE1" <-> "OE2" Residue "E ARG 176": "NH1" <-> "NH2" Residue "E ARG 194": "NH1" <-> "NH2" Residue "E ARG 197": "NH1" <-> "NH2" Residue "E ARG 207": "NH1" <-> "NH2" Residue "E GLU 211": "OE1" <-> "OE2" Residue "E ARG 327": "NH1" <-> "NH2" Residue "I GLU 17": "OE1" <-> "OE2" Residue "I GLU 27": "OE1" <-> "OE2" Residue "I TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 81": "OE1" <-> "OE2" Residue "J GLU 42": "OE1" <-> "OE2" Residue "J ARG 98": "NH1" <-> "NH2" Residue "J ARG 102": "NH1" <-> "NH2" Residue "L GLU 41": "OE1" <-> "OE2" Residue "L GLU 104": "OE1" <-> "OE2" Residue "K GLU 89": "OE1" <-> "OE2" Residue "K ARG 98": "NH1" <-> "NH2" Residue "K ARG 102": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 17399 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "B" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "C" Number of atoms: 2732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2732 Classifications: {'peptide': 334} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 318} Chain: "D" Number of atoms: 2730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2730 Classifications: {'peptide': 338} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 13, 'TRANS': 322} Chain: "E" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2729 Classifications: {'peptide': 333} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 318} Chain: "I" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 802 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 99} Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 907 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "L" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 811 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 100} Chain: "K" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 914 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen 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: 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: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 21 Unusual residues: {'ABU': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'ABU': 1, 'NAG': 1, 'UQA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen 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: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'UQA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.57, per 1000 atoms: 0.55 Number of scatterers: 17399 At special positions: 0 Unit cell: (141.075, 127.875, 136.125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 97 16.00 O 3235 8.00 N 2832 7.00 C 11235 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 136 " - pdb=" SG CYS A 150 " distance=2.03 Simple disulfide: pdb=" SG CYS B 139 " - pdb=" SG CYS B 153 " distance=2.03 Simple disulfide: pdb=" SG CYS C 136 " - pdb=" SG CYS C 150 " distance=2.02 Simple disulfide: pdb=" SG CYS D 139 " - pdb=" SG CYS D 153 " distance=2.03 Simple disulfide: pdb=" SG CYS E 151 " - pdb=" SG CYS E 165 " distance=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN G 5 " - " MAN G 6 " " MAN G 8 " - " MAN G 9 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 7 " - " MAN G 10 " ALPHA1-6 " BMA G 3 " - " MAN G 7 " " MAN G 7 " - " MAN G 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG M 1 " - " NAG M 2 " NAG-ASN " NAG A 404 " - " ASN A 80 " " NAG C 505 " - " ASN C 80 " " NAG D 401 " - " ASN D 111 " " NAG F 1 " - " ASN A 149 " " NAG G 1 " - " ASN B 111 " " NAG H 1 " - " ASN C 149 " " NAG M 1 " - " ASN E 208 " Time building additional restraints: 7.65 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: 34 helices and 28 sheets defined 28.1% alpha, 29.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'A' and resid 9 through 19 Processing helix chain 'A' and resid 85 through 89 Processing helix chain 'A' and resid 219 through 241 removed outlier: 5.038A pdb=" N MET A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Proline residue: A 228 - end of helix removed outlier: 4.380A pdb=" N SER A 239 " --> pdb=" O LEU A 235 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N PHE A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N TRP A 241 " --> pdb=" O TRP A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 271 Processing helix chain 'A' and resid 280 through 304 Processing helix chain 'A' and resid 310 through 338 removed outlier: 3.586A pdb=" N ALA A 314 " --> pdb=" O PRO A 310 " (cutoff:3.500A) Proline residue: A 325 - end of helix Processing helix chain 'B' and resid 13 through 22 Processing helix chain 'B' and resid 73 through 75 No H-bonds generated for 'chain 'B' and resid 73 through 75' Processing helix chain 'B' and resid 91 through 93 No H-bonds generated for 'chain 'B' and resid 91 through 93' Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 224 through 246 removed outlier: 3.993A pdb=" N ILE B 228 " --> pdb=" O GLY B 224 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU B 232 " --> pdb=" O ILE B 228 " (cutoff:3.500A) Proline residue: B 233 - end of helix removed outlier: 4.117A pdb=" N SER B 244 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N PHE B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TRP B 246 " --> pdb=" O GLN B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 276 removed outlier: 3.750A pdb=" N SER B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 310 Processing helix chain 'B' and resid 315 through 344 removed outlier: 3.986A pdb=" N ALA B 319 " --> pdb=" O PRO B 315 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE B 327 " --> pdb=" O ARG B 323 " (cutoff:3.500A) Proline residue: B 330 - end of helix Processing helix chain 'C' and resid 9 through 20 Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 219 through 241 removed outlier: 5.203A pdb=" N MET C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Proline residue: C 228 - end of helix removed outlier: 3.685A pdb=" N TRP C 237 " --> pdb=" O THR C 233 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL C 238 " --> pdb=" O ILE C 234 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N PHE C 240 " --> pdb=" O SER C 236 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N TRP C 241 " --> pdb=" O TRP C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 267 Processing helix chain 'C' and resid 280 through 304 Processing helix chain 'C' and resid 310 through 338 removed outlier: 3.662A pdb=" N ILE C 322 " --> pdb=" O ARG C 318 " (cutoff:3.500A) Proline residue: C 325 - end of helix Processing helix chain 'D' and resid 11 through 22 Processing helix chain 'D' and resid 175 through 177 No H-bonds generated for 'chain 'D' and resid 175 through 177' Processing helix chain 'D' and resid 224 through 246 removed outlier: 3.840A pdb=" N ILE D 228 " --> pdb=" O GLY D 224 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LEU D 232 " --> pdb=" O ILE D 228 " (cutoff:3.500A) Proline residue: D 233 - end of helix removed outlier: 4.039A pdb=" N SER D 244 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N PHE D 245 " --> pdb=" O SER D 241 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N TRP D 246 " --> pdb=" O GLN D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 252 through 274 Processing helix chain 'D' and resid 285 through 310 Processing helix chain 'D' and resid 315 through 345 removed outlier: 3.505A pdb=" N ARG D 326 " --> pdb=" O ASP D 322 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ILE D 327 " --> pdb=" O ARG D 323 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE D 329 " --> pdb=" O SER D 325 " (cutoff:3.500A) Proline residue: D 330 - end of helix Processing helix chain 'E' and resid 26 through 34 Processing helix chain 'E' and resid 100 through 105 removed outlier: 4.481A pdb=" N GLY E 104 " --> pdb=" O ASN E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 235 through 255 removed outlier: 5.545A pdb=" N ILE E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Proline residue: E 243 - end of helix removed outlier: 3.572A pdb=" N VAL E 253 " --> pdb=" O VAL E 249 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER E 254 " --> pdb=" O LEU E 250 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N PHE E 255 " --> pdb=" O SER E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 262 through 284 Processing helix chain 'E' and resid 297 through 323 removed outlier: 4.394A pdb=" N SER E 322 " --> pdb=" O HIS E 318 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER E 323 " --> pdb=" O TYR E 319 " (cutoff:3.500A) Processing helix chain 'E' and resid 325 through 356 removed outlier: 4.745A pdb=" N LYS E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET E 331 " --> pdb=" O ARG E 327 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASP E 332 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER E 333 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE E 337 " --> pdb=" O SER E 333 " (cutoff:3.500A) Proline residue: E 340 - end of helix Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'K' and resid 29 through 31 No H-bonds generated for 'chain 'K' and resid 29 through 31' Processing sheet with id= A, first strand: chain 'A' and resid 164 through 168 removed outlier: 6.316A pdb=" N VAL A 36 " --> pdb=" O GLU A 165 " (cutoff:3.500A) removed outlier: 7.824A pdb=" N TYR A 167 " --> pdb=" O VAL A 36 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N VAL A 38 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA A 37 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N ARG A 68 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N THR A 60 " --> pdb=" O ALA A 45 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE A 47 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR A 58 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ILE A 116 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 96 through 98 removed outlier: 3.816A pdb=" N CYS A 150 " --> pdb=" O PHE A 212 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N SER A 156 " --> pdb=" O PRO A 206 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASP A 190 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LYS A 215 " --> pdb=" O ILE A 188 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ILE A 188 " --> pdb=" O LYS A 215 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 101 through 106 removed outlier: 6.928A pdb=" N THR A 133 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N SER A 104 " --> pdb=" O THR A 131 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR A 131 " --> pdb=" O SER A 104 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 167 through 171 removed outlier: 6.176A pdb=" N THR B 39 " --> pdb=" O VAL B 168 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N GLU B 170 " --> pdb=" O THR B 39 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N VAL B 41 " --> pdb=" O GLU B 170 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU B 40 " --> pdb=" O LYS B 71 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N LYS B 71 " --> pdb=" O GLU B 40 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ASP B 63 " --> pdb=" O THR B 48 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE B 50 " --> pdb=" O THR B 61 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR B 61 " --> pdb=" O PHE B 50 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N THR B 126 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU B 119 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 45 through 47 Processing sheet with id= F, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.064A pdb=" N SER B 159 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL B 211 " --> pdb=" O SER B 159 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY B 195 " --> pdb=" O HIS B 218 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS B 220 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N LEU B 193 " --> pdb=" O LYS B 220 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 164 through 168 removed outlier: 6.423A pdb=" N VAL C 36 " --> pdb=" O GLU C 165 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N TYR C 167 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL C 38 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ALA C 37 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ARG C 68 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR C 60 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ILE C 47 " --> pdb=" O THR C 58 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR C 58 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ILE C 116 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU C 83 " --> pdb=" O ILE C 116 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 96 through 98 removed outlier: 3.762A pdb=" N SER C 156 " --> pdb=" O PRO C 206 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ASP C 190 " --> pdb=" O LYS C 213 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N LYS C 215 " --> pdb=" O ILE C 188 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ILE C 188 " --> pdb=" O LYS C 215 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 101 through 106 removed outlier: 6.829A pdb=" N THR C 133 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N SER C 104 " --> pdb=" O THR C 131 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N THR C 131 " --> pdb=" O SER C 104 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 167 through 171 removed outlier: 6.266A pdb=" N THR D 39 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 7.648A pdb=" N GLU D 170 " --> pdb=" O THR D 39 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N VAL D 41 " --> pdb=" O GLU D 170 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU D 40 " --> pdb=" O LYS D 71 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N LYS D 71 " --> pdb=" O GLU D 40 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP D 63 " --> pdb=" O THR D 48 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N PHE D 50 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR D 61 " --> pdb=" O PHE D 50 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR D 126 " --> pdb=" O THR D 122 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N LEU D 119 " --> pdb=" O LEU D 86 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 45 through 47 Processing sheet with id= L, first strand: chain 'D' and resid 99 through 101 Processing sheet with id= M, first strand: chain 'D' and resid 150 through 154 removed outlier: 3.915A pdb=" N GLY D 195 " --> pdb=" O HIS D 218 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS D 220 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LEU D 193 " --> pdb=" O LYS D 220 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 179 through 183 removed outlier: 5.733A pdb=" N THR E 51 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N GLN E 182 " --> pdb=" O THR E 51 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ILE E 53 " --> pdb=" O GLN E 182 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LEU E 52 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N TYR E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ARG E 138 " --> pdb=" O TRP E 134 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU E 131 " --> pdb=" O LEU E 98 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 188 through 190 removed outlier: 6.622A pdb=" N MET E 57 " --> pdb=" O GLU E 189 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ASP E 75 " --> pdb=" O ASN E 60 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 111 through 113 removed outlier: 3.617A pdb=" N PHE E 227 " --> pdb=" O CYS E 165 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER E 171 " --> pdb=" O VAL E 221 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N VAL E 221 " --> pdb=" O SER E 171 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY E 205 " --> pdb=" O ASP E 228 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N SER E 230 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N PHE E 203 " --> pdb=" O SER E 230 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 116 through 121 removed outlier: 7.040A pdb=" N ASP E 148 " --> pdb=" O LYS E 117 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ALA E 119 " --> pdb=" O THR E 146 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N THR E 146 " --> pdb=" O ALA E 119 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'I' and resid 4 through 7 Processing sheet with id= S, first strand: chain 'I' and resid 10 through 12 removed outlier: 6.473A pdb=" N LYS I 102 " --> pdb=" O MET I 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'I' and resid 85 through 90 removed outlier: 6.265A pdb=" N GLN I 37 " --> pdb=" O LEU I 46 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LEU I 46 " --> pdb=" O GLN I 37 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 3 through 6 Processing sheet with id= V, first strand: chain 'J' and resid 10 through 12 removed outlier: 3.517A pdb=" N GLY J 49 " --> pdb=" O TRP J 36 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N LYS J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N TRP J 47 " --> pdb=" O LYS J 38 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'L' and resid 4 through 7 Processing sheet with id= X, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.069A pdb=" N LYS L 102 " --> pdb=" O MET L 11 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N MET L 13 " --> pdb=" O LYS L 102 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N GLU L 104 " --> pdb=" O MET L 13 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'L' and resid 85 through 90 removed outlier: 6.180A pdb=" N GLN L 37 " --> pdb=" O LEU L 46 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU L 46 " --> pdb=" O GLN L 37 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'K' and resid 3 through 6 Processing sheet with id= AA, first strand: chain 'K' and resid 10 through 12 Processing sheet with id= AB, first strand: chain 'K' and resid 57 through 60 removed outlier: 3.671A pdb=" N ASP K 57 " --> pdb=" O ASP K 52 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N MET K 34 " --> pdb=" O ARG K 50 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N TYR K 33 " --> pdb=" O LYS K 99 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR K 107 " --> pdb=" O ARG K 98 " (cutoff:3.500A) 739 hydrogen bonds defined for protein. 2157 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.34 Time building geometry restraints manager: 7.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4373 1.33 - 1.46: 4820 1.46 - 1.58: 8475 1.58 - 1.71: 0 1.71 - 1.83: 167 Bond restraints: 17835 Sorted by residual: bond pdb=" CD ABU A 405 " pdb=" OE2 ABU A 405 " ideal model delta sigma weight residual 1.250 1.333 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" CD ABU C 506 " pdb=" OE2 ABU C 506 " ideal model delta sigma weight residual 1.250 1.333 -0.083 2.00e-02 2.50e+03 1.72e+01 bond pdb=" C MET D 114 " pdb=" N PRO D 115 " ideal model delta sigma weight residual 1.332 1.374 -0.042 1.12e-02 7.97e+03 1.41e+01 bond pdb=" C VAL D 252 " pdb=" N PRO D 253 " ideal model delta sigma weight residual 1.335 1.373 -0.039 1.28e-02 6.10e+03 9.07e+00 bond pdb=" C THR E 125 " pdb=" N THR E 126 " ideal model delta sigma weight residual 1.333 1.292 0.042 1.39e-02 5.18e+03 8.99e+00 ... (remaining 17830 not shown) Histogram of bond angle deviations from ideal: 95.19 - 103.08: 129 103.08 - 110.98: 6275 110.98 - 118.88: 7974 118.88 - 126.77: 9615 126.77 - 134.67: 263 Bond angle restraints: 24256 Sorted by residual: angle pdb=" N ARG C 269 " pdb=" CA ARG C 269 " pdb=" C ARG C 269 " ideal model delta sigma weight residual 113.41 104.73 8.68 1.22e+00 6.72e-01 5.07e+01 angle pdb=" C THR C 271 " pdb=" N LEU C 272 " pdb=" CA LEU C 272 " ideal model delta sigma weight residual 123.96 133.94 -9.98 1.44e+00 4.82e-01 4.80e+01 angle pdb=" N ILE C 322 " pdb=" CA ILE C 322 " pdb=" C ILE C 322 " ideal model delta sigma weight residual 112.96 107.97 4.99 1.00e+00 1.00e+00 2.49e+01 angle pdb=" CA GLU C 147 " pdb=" CB GLU C 147 " pdb=" CG GLU C 147 " ideal model delta sigma weight residual 114.10 123.27 -9.17 2.00e+00 2.50e-01 2.10e+01 angle pdb=" N LEU C 152 " pdb=" CA LEU C 152 " pdb=" C LEU C 152 " ideal model delta sigma weight residual 108.34 100.95 7.39 1.64e+00 3.72e-01 2.03e+01 ... (remaining 24251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 9386 17.97 - 35.94: 792 35.94 - 53.90: 140 53.90 - 71.87: 16 71.87 - 89.84: 13 Dihedral angle restraints: 10347 sinusoidal: 4091 harmonic: 6256 Sorted by residual: dihedral pdb=" CB CYS A 136 " pdb=" SG CYS A 136 " pdb=" SG CYS A 150 " pdb=" CB CYS A 150 " ideal model delta sinusoidal sigma weight residual -86.00 -9.25 -76.75 1 1.00e+01 1.00e-02 7.40e+01 dihedral pdb=" CB CYS E 151 " pdb=" SG CYS E 151 " pdb=" SG CYS E 165 " pdb=" CB CYS E 165 " ideal model delta sinusoidal sigma weight residual -86.00 -12.15 -73.85 1 1.00e+01 1.00e-02 6.93e+01 dihedral pdb=" CA CYS C 150 " pdb=" C CYS C 150 " pdb=" N THR C 151 " pdb=" CA THR C 151 " ideal model delta harmonic sigma weight residual -180.00 -151.89 -28.11 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 10344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.283: 2784 0.283 - 0.565: 9 0.565 - 0.848: 4 0.848 - 1.130: 1 1.130 - 1.413: 1 Chirality restraints: 2799 Sorted by residual: chirality pdb=" C1 BMA F 3 " pdb=" O4 NAG F 2 " pdb=" C2 BMA F 3 " pdb=" O5 BMA F 3 " both_signs ideal model delta sigma weight residual False -2.40 -0.99 -1.41 2.00e-02 2.50e+03 4.99e+03 chirality pdb=" C1 BMA H 3 " pdb=" O4 NAG H 2 " pdb=" C2 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.40 -1.62 -0.78 2.00e-02 2.50e+03 1.52e+03 chirality pdb=" C1 MAN G 9 " pdb=" O2 MAN G 8 " pdb=" C2 MAN G 9 " pdb=" O5 MAN G 9 " both_signs ideal model delta sigma weight residual False 2.40 1.64 0.76 2.00e-02 2.50e+03 1.46e+03 ... (remaining 2796 not shown) Planarity restraints: 2992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 2 " 0.193 2.00e-02 2.50e+03 1.59e-01 3.17e+02 pdb=" C7 NAG M 2 " -0.052 2.00e-02 2.50e+03 pdb=" C8 NAG M 2 " 0.140 2.00e-02 2.50e+03 pdb=" N2 NAG M 2 " -0.258 2.00e-02 2.50e+03 pdb=" O7 NAG M 2 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG M 1 " -0.180 2.00e-02 2.50e+03 1.53e-01 2.93e+02 pdb=" C7 NAG M 1 " 0.037 2.00e-02 2.50e+03 pdb=" C8 NAG M 1 " 0.036 2.00e-02 2.50e+03 pdb=" N2 NAG M 1 " 0.249 2.00e-02 2.50e+03 pdb=" O7 NAG M 1 " -0.142 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG G 2 " -0.129 2.00e-02 2.50e+03 1.06e-01 1.41e+02 pdb=" C7 NAG G 2 " 0.034 2.00e-02 2.50e+03 pdb=" C8 NAG G 2 " -0.096 2.00e-02 2.50e+03 pdb=" N2 NAG G 2 " 0.171 2.00e-02 2.50e+03 pdb=" O7 NAG G 2 " 0.020 2.00e-02 2.50e+03 ... (remaining 2989 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1981 2.75 - 3.29: 15940 3.29 - 3.82: 29721 3.82 - 4.36: 36301 4.36 - 4.90: 63788 Nonbonded interactions: 147731 Sorted by model distance: nonbonded pdb=" OD1 ASP E 120 " pdb=" O4 MAN G 10 " model vdw 2.211 2.440 nonbonded pdb=" OD2 ASP A 121 " pdb=" OG1 THR A 123 " model vdw 2.269 2.440 nonbonded pdb=" O ALA E 295 " pdb=" OH TYR E 350 " model vdw 2.281 2.440 nonbonded pdb=" OH TYR D 26 " pdb=" OD2 ASP D 72 " model vdw 2.283 2.440 nonbonded pdb=" OG1 THR B 99 " pdb=" OH TYR B 169 " model vdw 2.289 2.440 ... (remaining 147726 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 7 through 340) selection = (chain 'C' and resid 7 through 340) } ncs_group { reference = chain 'B' selection = (chain 'D' and resid 10 through 347) } ncs_group { reference = chain 'F' selection = chain 'H' } ncs_group { reference = chain 'I' selection = (chain 'L' and resid 1 through 105) } ncs_group { reference = chain 'J' selection = (chain 'K' and resid 2 through 117) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 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: 7.940 Check model and map are aligned: 0.250 Set scattering table: 0.150 Process input model: 46.510 Find NCS groups from input model: 1.070 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: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.083 17835 Z= 0.509 Angle : 1.158 13.492 24256 Z= 0.640 Chirality : 0.082 1.413 2799 Planarity : 0.008 0.159 2985 Dihedral : 13.451 89.841 6300 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer Outliers : 0.85 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.16), residues: 2103 helix: -0.16 (0.20), residues: 581 sheet: -1.01 (0.19), residues: 623 loop : -2.41 (0.17), residues: 899 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4206 Ramachandran restraints generated. 2103 Oldfield, 0 Emsley, 2103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 411 time to evaluate : 1.835 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 421 average time/residue: 0.3364 time to fit residues: 203.7222 Evaluate side-chains 336 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 326 time to evaluate : 2.166 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1618 time to fit residues: 6.1706 ------------------------------------------------------------------------------- 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: 1.9990 chunk 156 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 162 optimal weight: 10.0000 chunk 62 optimal weight: 0.9980 chunk 98 optimal weight: 4.9990 chunk 120 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 ASN A 65 GLN A 185 GLN A 303 ASN B 68 GLN B 142 HIS B 189 ASN B 275 ASN B 308 ASN C 41 ASN C 54 ASN C 65 GLN D 68 GLN D 102 HIS E 60 ASN E 80 GLN E 128 ASN E 163 HIS E 258 ASN E 318 HIS J 6 GLN L 42 GLN L 53 ASN K 6 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 17835 Z= 0.220 Angle : 0.582 9.338 24256 Z= 0.297 Chirality : 0.044 0.250 2799 Planarity : 0.004 0.041 2985 Dihedral : 4.489 28.665 2360 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % 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: -1.31 (0.17), residues: 2103 helix: 0.50 (0.21), residues: 585 sheet: -0.82 (0.18), residues: 636 loop : -1.80 (0.19), residues: 882 *********************** 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 386 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 349 time to evaluate : 2.217 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 29 residues processed: 365 average time/residue: 0.3244 time to fit residues: 173.5672 Evaluate side-chains 356 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 327 time to evaluate : 2.125 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1660 time to fit residues: 11.7835 ------------------------------------------------------------------------------- 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: 0.7980 chunk 58 optimal weight: 10.0000 chunk 156 optimal weight: 0.8980 chunk 128 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 188 optimal weight: 0.9990 chunk 203 optimal weight: 8.9990 chunk 167 optimal weight: 3.9990 chunk 186 optimal weight: 0.0470 chunk 64 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 overall best weight: 0.7482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN D 88 ASN E 318 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 17835 Z= 0.171 Angle : 0.535 9.569 24256 Z= 0.272 Chirality : 0.042 0.260 2799 Planarity : 0.004 0.036 2985 Dihedral : 4.305 26.636 2360 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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: -0.92 (0.17), residues: 2103 helix: 0.85 (0.21), residues: 588 sheet: -0.79 (0.19), residues: 627 loop : -1.40 (0.19), residues: 888 *********************** 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 367 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 337 time to evaluate : 2.018 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 18 residues processed: 357 average time/residue: 0.3170 time to fit residues: 167.2903 Evaluate side-chains 331 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 313 time to evaluate : 2.133 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1616 time to fit residues: 8.3585 ------------------------------------------------------------------------------- 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: 7.9990 chunk 141 optimal weight: 5.9990 chunk 97 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 89 optimal weight: 0.9980 chunk 126 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 chunk 200 optimal weight: 7.9990 chunk 98 optimal weight: 0.8980 chunk 179 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN E 318 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 17835 Z= 0.186 Angle : 0.529 9.498 24256 Z= 0.268 Chirality : 0.042 0.256 2799 Planarity : 0.004 0.036 2985 Dihedral : 4.224 26.232 2360 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: -0.61 (0.18), residues: 2103 helix: 1.08 (0.21), residues: 582 sheet: -0.68 (0.19), residues: 639 loop : -1.12 (0.20), residues: 882 *********************** 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 364 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 327 time to evaluate : 2.140 Fit side-chains revert: symmetry clash outliers start: 37 outliers final: 26 residues processed: 349 average time/residue: 0.3136 time to fit residues: 163.1967 Evaluate side-chains 340 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 314 time to evaluate : 2.019 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.1593 time to fit residues: 10.3997 ------------------------------------------------------------------------------- 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: 7.9990 chunk 113 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 148 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 170 optimal weight: 0.0870 chunk 138 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 179 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.5162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 185 GLN B 116 ASN C 41 ASN E 318 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 17835 Z= 0.262 Angle : 0.555 9.480 24256 Z= 0.282 Chirality : 0.043 0.258 2799 Planarity : 0.004 0.040 2985 Dihedral : 4.312 25.867 2360 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % 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: -0.47 (0.18), residues: 2103 helix: 1.21 (0.22), residues: 581 sheet: -0.72 (0.19), residues: 635 loop : -0.93 (0.20), residues: 887 *********************** 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 355 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 324 time to evaluate : 2.064 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 340 average time/residue: 0.3182 time to fit residues: 161.2776 Evaluate side-chains 329 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 311 time to evaluate : 2.213 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1601 time to fit residues: 8.3362 ------------------------------------------------------------------------------- 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: 0.0570 chunk 39 optimal weight: 0.7980 chunk 117 optimal weight: 0.0980 chunk 49 optimal weight: 1.9990 chunk 200 optimal weight: 6.9990 chunk 166 optimal weight: 8.9990 chunk 92 optimal weight: 0.0970 chunk 16 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 116 ASN B 308 ASN ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.049 17835 Z= 0.135 Angle : 0.510 9.502 24256 Z= 0.259 Chirality : 0.041 0.258 2799 Planarity : 0.003 0.039 2985 Dihedral : 4.121 26.165 2360 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer Outliers : 1.43 % 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: -0.26 (0.18), residues: 2103 helix: 1.36 (0.21), residues: 581 sheet: -0.60 (0.19), residues: 636 loop : -0.78 (0.21), residues: 886 *********************** 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 360 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 333 time to evaluate : 2.235 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 16 residues processed: 346 average time/residue: 0.3217 time to fit residues: 164.6915 Evaluate side-chains 337 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 321 time to evaluate : 2.072 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1671 time to fit residues: 7.7311 ------------------------------------------------------------------------------- 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: 2.9990 chunk 114 optimal weight: 0.8980 chunk 146 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 168 optimal weight: 5.9990 chunk 111 optimal weight: 5.9990 chunk 199 optimal weight: 8.9990 chunk 124 optimal weight: 0.9980 chunk 121 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 224 GLN B 116 ASN E 318 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 17835 Z= 0.234 Angle : 0.542 9.497 24256 Z= 0.275 Chirality : 0.043 0.258 2799 Planarity : 0.004 0.041 2985 Dihedral : 4.201 25.489 2360 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % 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: -0.26 (0.18), residues: 2103 helix: 1.36 (0.21), residues: 580 sheet: -0.64 (0.19), residues: 630 loop : -0.74 (0.21), residues: 893 *********************** 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 342 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 319 time to evaluate : 2.121 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 16 residues processed: 333 average time/residue: 0.3149 time to fit residues: 155.9379 Evaluate side-chains 326 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 310 time to evaluate : 2.070 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1651 time to fit residues: 7.7736 ------------------------------------------------------------------------------- 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: 0.0770 chunk 79 optimal weight: 0.1980 chunk 119 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 135 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 overall best weight: 0.6140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 224 GLN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 ASN C 41 ASN C 224 GLN E 101 ASN E 318 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 17835 Z= 0.156 Angle : 0.524 9.567 24256 Z= 0.265 Chirality : 0.042 0.255 2799 Planarity : 0.003 0.041 2985 Dihedral : 4.138 25.813 2360 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: -0.10 (0.18), residues: 2103 helix: 1.43 (0.21), residues: 580 sheet: -0.45 (0.19), residues: 628 loop : -0.69 (0.21), residues: 895 *********************** 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 341 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 325 time to evaluate : 2.312 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 331 average time/residue: 0.3131 time to fit residues: 154.6169 Evaluate side-chains 326 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 315 time to evaluate : 2.157 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1685 time to fit residues: 6.5113 ------------------------------------------------------------------------------- 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: 0.1980 chunk 191 optimal weight: 0.0670 chunk 174 optimal weight: 2.9990 chunk 185 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 145 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 168 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 overall best weight: 0.6120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 224 GLN B 116 ASN B 308 ASN C 41 ASN ** C 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 101 ASN E 318 HIS K 3 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 17835 Z= 0.157 Angle : 0.522 10.470 24256 Z= 0.264 Chirality : 0.042 0.255 2799 Planarity : 0.003 0.039 2985 Dihedral : 4.061 25.660 2360 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % 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: 0.00 (0.18), residues: 2103 helix: 1.49 (0.22), residues: 580 sheet: -0.35 (0.20), residues: 630 loop : -0.63 (0.21), residues: 893 *********************** 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 336 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 325 time to evaluate : 2.545 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 7 residues processed: 330 average time/residue: 0.3136 time to fit residues: 154.0494 Evaluate side-chains 317 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 310 time to evaluate : 1.990 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.1754 time to fit residues: 4.9163 ------------------------------------------------------------------------------- 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: 0.0570 chunk 119 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 206 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 17 optimal weight: 0.2980 chunk 126 optimal weight: 0.9990 chunk 100 optimal weight: 0.0970 chunk 130 optimal weight: 9.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 224 GLN B 116 ASN B 190 GLN B 308 ASN C 41 ASN C 224 GLN ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 17835 Z= 0.143 Angle : 0.520 11.066 24256 Z= 0.263 Chirality : 0.041 0.255 2799 Planarity : 0.003 0.040 2985 Dihedral : 4.012 25.190 2360 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % 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: 0.09 (0.18), residues: 2103 helix: 1.67 (0.22), residues: 568 sheet: -0.32 (0.20), residues: 660 loop : -0.62 (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 323 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 314 time to evaluate : 2.213 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 316 average time/residue: 0.3097 time to fit residues: 145.8219 Evaluate side-chains 311 residues out of total 1883 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 305 time to evaluate : 2.009 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1692 time to fit residues: 4.5474 ------------------------------------------------------------------------------- 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: 0.0970 chunk 50 optimal weight: 7.9990 chunk 151 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 164 optimal weight: 4.9990 chunk 68 optimal weight: 0.2980 chunk 168 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN A 224 GLN ** B 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 HIS B 190 GLN B 308 ASN C 41 ASN ** D 242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 318 HIS J 43 GLN L 37 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.131714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.103846 restraints weight = 21212.639| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.75 r_work: 0.2867 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 17835 Z= 0.261 Angle : 0.565 11.122 24256 Z= 0.285 Chirality : 0.043 0.259 2799 Planarity : 0.004 0.041 2985 Dihedral : 4.209 25.033 2360 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.05 % Cis-general : 0.25 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2103 helix: 1.46 (0.21), residues: 582 sheet: -0.39 (0.20), residues: 624 loop : -0.57 (0.21), residues: 897 =============================================================================== Job complete usr+sys time: 4081.24 seconds wall clock time: 74 minutes 51.59 seconds (4491.59 seconds total)