Starting phenix.real_space_refine on Tue Apr 7 18:43:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ec7_47901/04_2026/9ec7_47901_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ec7_47901/04_2026/9ec7_47901.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ec7_47901/04_2026/9ec7_47901_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ec7_47901/04_2026/9ec7_47901_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ec7_47901/04_2026/9ec7_47901.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ec7_47901/04_2026/9ec7_47901.map" } resolution = 3.76 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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: 5 Type Number sf(0) Gaussians S 51 5.16 5 C 9266 2.51 5 N 2428 2.21 5 O 3013 1.98 5 H 14176 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28934 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3390 Classifications: {'peptide': 228} Link IDs: {'PTRANS': 14, 'TRANS': 213} Chain: "B" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3320 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "C" Number of atoms: 3391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 3391 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 213} Chain: "D" Number of atoms: 3333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3333 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 14, 'TRANS': 209} Chain: "E" Number of atoms: 3320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 3320 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 14, 'TRANS': 208} Chain: "F" Number of atoms: 3311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 3311 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 14, 'TRANS': 207} Chain: "G" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 3299 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 14, 'TRANS': 206} Chain: "H" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3289 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 14, 'TRANS': 205} Chain: "J" Number of atoms: 2019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 2019 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 9, 'TRANS': 118} Chain: "L" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "Q" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "K" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.63, per 1000 atoms: 0.19 Number of scatterers: 28934 At special positions: 0 Unit cell: (66.402, 144.398, 184.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 51 16.00 O 3013 8.00 N 2428 7.00 C 9266 6.00 H 14176 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS A 235 " - pdb=" SG CYS A 292 " distance=2.03 Simple disulfide: pdb=" SG CYS A 340 " - pdb=" SG CYS A 400 " distance=2.03 Simple disulfide: pdb=" SG CYS A 439 " - pdb=" SG CYS J 73 " distance=2.03 Simple disulfide: pdb=" SG CYS B 235 " - pdb=" SG CYS B 292 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS E 280 " distance=2.03 Simple disulfide: pdb=" SG CYS B 340 " - pdb=" SG CYS B 400 " distance=2.03 Simple disulfide: pdb=" SG CYS C 235 " - pdb=" SG CYS C 292 " distance=2.03 Simple disulfide: pdb=" SG CYS C 340 " - pdb=" SG CYS C 400 " distance=2.03 Simple disulfide: pdb=" SG CYS D 235 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS D 340 " - pdb=" SG CYS D 400 " distance=2.03 Simple disulfide: pdb=" SG CYS E 235 " - pdb=" SG CYS E 292 " distance=2.03 Simple disulfide: pdb=" SG CYS E 340 " - pdb=" SG CYS E 400 " distance=2.03 Simple disulfide: pdb=" SG CYS F 235 " - pdb=" SG CYS F 292 " distance=2.03 Simple disulfide: pdb=" SG CYS F 340 " - pdb=" SG CYS F 400 " distance=2.03 Simple disulfide: pdb=" SG CYS G 235 " - pdb=" SG CYS G 292 " distance=2.03 Simple disulfide: pdb=" SG CYS G 340 " - pdb=" SG CYS G 400 " distance=2.03 Simple disulfide: pdb=" SG CYS H 235 " - pdb=" SG CYS H 292 " distance=2.03 Simple disulfide: pdb=" SG CYS H 340 " - pdb=" SG CYS H 400 " distance=2.03 Simple disulfide: pdb=" SG CYS J 17 " - pdb=" SG CYS J 102 " distance=2.03 Simple disulfide: pdb=" SG CYS J 76 " - pdb=" SG CYS J 96 " distance=2.03 Simple disulfide: pdb=" SG CYS J 110 " - pdb=" SG CYS J 135 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 BETA1-4 " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " NAG-ASN " NAG K 1 " - " ASN B 230 " " NAG L 1 " - " ASN C 230 " " NAG M 1 " - " ASN D 230 " " NAG N 1 " - " ASN E 230 " " NAG O 1 " - " ASN F 230 " " NAG P 1 " - " ASN G 230 " " NAG Q 1 " - " ASN J 53 " Time building additional restraints: 2.52 Conformation dependent library (CDL) restraints added in 871.5 milliseconds 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3572 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 44 sheets defined 15.1% alpha, 36.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 221 through 228 Processing helix chain 'A' and resid 266 through 270 removed outlier: 4.025A pdb=" N LEU A 270 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 326 through 332 Processing helix chain 'A' and resid 388 through 395 removed outlier: 3.566A pdb=" N TRP A 392 " --> pdb=" O ALA A 388 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY A 395 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.911A pdb=" N LEU B 270 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 286 Processing helix chain 'B' and resid 326 through 333 Processing helix chain 'B' and resid 374 through 378 Processing helix chain 'B' and resid 389 through 394 Processing helix chain 'C' and resid 221 through 227 removed outlier: 3.551A pdb=" N TYR C 226 " --> pdb=" O LEU C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 270 removed outlier: 3.809A pdb=" N LEU C 270 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 286 Processing helix chain 'C' and resid 326 through 333 Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 417 through 421 Processing helix chain 'D' and resid 221 through 227 Processing helix chain 'D' and resid 266 through 270 removed outlier: 3.824A pdb=" N LEU D 270 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 286 Processing helix chain 'D' and resid 326 through 333 Processing helix chain 'D' and resid 374 through 378 Processing helix chain 'D' and resid 388 through 394 removed outlier: 3.750A pdb=" N TRP D 392 " --> pdb=" O ALA D 388 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 227 Processing helix chain 'E' and resid 266 through 270 removed outlier: 4.007A pdb=" N LEU E 270 " --> pdb=" O GLU E 267 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 286 Processing helix chain 'E' and resid 326 through 332 Processing helix chain 'E' and resid 362 through 364 No H-bonds generated for 'chain 'E' and resid 362 through 364' Processing helix chain 'E' and resid 388 through 395 Processing helix chain 'F' and resid 221 through 226 Processing helix chain 'F' and resid 280 through 286 Processing helix chain 'F' and resid 326 through 333 Processing helix chain 'F' and resid 388 through 394 removed outlier: 3.504A pdb=" N TRP F 392 " --> pdb=" O ALA F 388 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 228 Processing helix chain 'G' and resid 266 through 270 removed outlier: 3.833A pdb=" N LEU G 270 " --> pdb=" O GLU G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 286 Processing helix chain 'G' and resid 326 through 333 Processing helix chain 'G' and resid 389 through 394 Processing helix chain 'H' and resid 221 through 227 Processing helix chain 'H' and resid 266 through 270 removed outlier: 3.902A pdb=" N LEU H 270 " --> pdb=" O GLU H 267 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 286 Processing helix chain 'H' and resid 326 through 333 Processing helix chain 'H' and resid 362 through 366 Processing helix chain 'H' and resid 388 through 394 removed outlier: 3.733A pdb=" N TRP H 392 " --> pdb=" O ALA H 388 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 74 removed outlier: 3.542A pdb=" N CYS J 73 " --> pdb=" O MET J 69 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS J 74 " --> pdb=" O ALA J 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 69 through 74' Processing sheet with id=AA1, first strand: chain 'A' and resid 214 through 218 removed outlier: 3.671A pdb=" N VAL A 233 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU A 273 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 274 " --> pdb=" O GLY A 261 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 259 " --> pdb=" O VAL A 276 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 245 through 250 Processing sheet with id=AA3, first strand: chain 'A' and resid 321 through 323 Processing sheet with id=AA4, first strand: chain 'A' and resid 321 through 323 removed outlier: 5.722A pdb=" N PHE A 379 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLY A 374 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 359 through 360 removed outlier: 3.547A pdb=" N PHE A 398 " --> pdb=" O LEU A 416 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 428 removed outlier: 6.370A pdb=" N VAL A 426 " --> pdb=" O ASN B 427 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N VAL B 426 " --> pdb=" O ASN E 427 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER E 429 " --> pdb=" O VAL B 426 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL B 428 " --> pdb=" O SER E 429 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N VAL E 431 " --> pdb=" O VAL B 428 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N VAL E 426 " --> pdb=" O ASN F 427 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N SER F 429 " --> pdb=" O VAL E 426 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL E 428 " --> pdb=" O SER F 429 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N VAL F 431 " --> pdb=" O VAL E 428 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL E 430 " --> pdb=" O VAL F 431 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 430 through 433 removed outlier: 6.689A pdb=" N VAL A 431 " --> pdb=" O TYR J 67 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 232 through 237 removed outlier: 3.583A pdb=" N LEU B 273 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 245 through 250 Processing sheet with id=AB1, first strand: chain 'B' and resid 319 through 323 removed outlier: 3.542A pdb=" N THR B 339 " --> pdb=" O PHE B 323 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER B 383 " --> pdb=" O CYS B 340 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 319 through 323 removed outlier: 3.542A pdb=" N THR B 339 " --> pdb=" O PHE B 323 " (cutoff:3.500A) removed outlier: 6.131A pdb=" N PHE B 379 " --> pdb=" O GLY B 344 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 351 through 356 removed outlier: 3.521A pdb=" N PHE B 398 " --> pdb=" O LEU B 416 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 214 through 218 removed outlier: 3.501A pdb=" N THR C 234 " --> pdb=" O LEU C 218 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N VAL C 259 " --> pdb=" O VAL C 276 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 245 through 250 Processing sheet with id=AB6, first strand: chain 'C' and resid 319 through 323 removed outlier: 3.691A pdb=" N THR C 339 " --> pdb=" O PHE C 323 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 338 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU C 385 " --> pdb=" O LEU C 338 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER C 383 " --> pdb=" O CYS C 340 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 319 through 323 removed outlier: 3.691A pdb=" N THR C 339 " --> pdb=" O PHE C 323 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY C 344 " --> pdb=" O PHE C 379 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N PHE C 379 " --> pdb=" O GLY C 344 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU C 375 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N SER C 380 " --> pdb=" O GLU C 373 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLU C 373 " --> pdb=" O SER C 380 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 351 through 356 removed outlier: 3.748A pdb=" N ALA C 399 " --> pdb=" O THR C 355 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LYS C 414 " --> pdb=" O CYS C 400 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 424 through 426 removed outlier: 3.597A pdb=" N VAL D 428 " --> pdb=" O ASN G 427 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL C 426 " --> pdb=" O ASN D 427 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N SER D 429 " --> pdb=" O VAL C 426 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL C 428 " --> pdb=" O SER D 429 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N VAL D 431 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N VAL C 430 " --> pdb=" O VAL D 431 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLN C 425 " --> pdb=" O LEU J 38 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER C 433 " --> pdb=" O VAL J 46 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 214 through 218 removed outlier: 3.521A pdb=" N THR D 234 " --> pdb=" O LEU D 218 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N THR D 234 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N LEU D 277 " --> pdb=" O THR D 234 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N VAL D 236 " --> pdb=" O SER D 275 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N SER D 275 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N THR D 238 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU D 273 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D 240 " --> pdb=" O TYR D 271 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 249 through 250 Processing sheet with id=AC3, first strand: chain 'D' and resid 319 through 323 removed outlier: 3.599A pdb=" N THR D 339 " --> pdb=" O PHE D 323 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL D 387 " --> pdb=" O ALA D 336 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU D 338 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N SER D 383 " --> pdb=" O CYS D 340 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS D 384 " --> pdb=" O SER D 367 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 319 through 323 removed outlier: 3.599A pdb=" N THR D 339 " --> pdb=" O PHE D 323 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 351 through 354 removed outlier: 3.680A pdb=" N LYS D 414 " --> pdb=" O CYS D 400 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 214 through 218 removed outlier: 5.882A pdb=" N THR E 234 " --> pdb=" O LEU E 277 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU E 277 " --> pdb=" O THR E 234 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N VAL E 236 " --> pdb=" O SER E 275 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N SER E 275 " --> pdb=" O VAL E 236 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N THR E 238 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N LEU E 273 " --> pdb=" O THR E 238 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ALA E 240 " --> pdb=" O TYR E 271 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR E 274 " --> pdb=" O GLY E 261 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 245 through 250 removed outlier: 3.719A pdb=" N LYS E 305 " --> pdb=" O CYS E 292 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 319 through 323 removed outlier: 3.641A pdb=" N THR E 339 " --> pdb=" O PHE E 323 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE E 379 " --> pdb=" O GLY E 344 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 319 through 323 removed outlier: 3.641A pdb=" N THR E 339 " --> pdb=" O PHE E 323 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE E 379 " --> pdb=" O GLY E 344 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N SER E 380 " --> pdb=" O GLU E 373 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLU E 373 " --> pdb=" O SER E 380 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 359 through 360 Processing sheet with id=AD2, first strand: chain 'F' and resid 214 through 216 removed outlier: 3.548A pdb=" N THR F 238 " --> pdb=" O GLU F 214 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL F 233 " --> pdb=" O LEU F 277 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL F 276 " --> pdb=" O VAL F 259 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 249 through 250 Processing sheet with id=AD4, first strand: chain 'F' and resid 319 through 323 removed outlier: 3.586A pdb=" N SER F 343 " --> pdb=" O SER F 319 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR F 339 " --> pdb=" O PHE F 323 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 319 through 323 removed outlier: 3.586A pdb=" N SER F 343 " --> pdb=" O SER F 319 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR F 339 " --> pdb=" O PHE F 323 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY F 344 " --> pdb=" O PHE F 379 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE F 379 " --> pdb=" O GLY F 344 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'F' and resid 351 through 355 Processing sheet with id=AD7, first strand: chain 'G' and resid 214 through 218 Processing sheet with id=AD8, first strand: chain 'G' and resid 245 through 250 Processing sheet with id=AD9, first strand: chain 'G' and resid 319 through 323 Processing sheet with id=AE1, first strand: chain 'G' and resid 319 through 323 removed outlier: 6.184A pdb=" N PHE G 379 " --> pdb=" O GLY G 344 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 359 through 360 removed outlier: 3.613A pdb=" N LYS G 414 " --> pdb=" O CYS G 400 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 214 through 218 removed outlier: 3.539A pdb=" N LEU H 273 " --> pdb=" O ALA H 237 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 245 through 247 removed outlier: 3.576A pdb=" N PHE H 290 " --> pdb=" O VAL H 307 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL H 307 " --> pdb=" O PHE H 290 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'H' and resid 319 through 323 removed outlier: 4.098A pdb=" N GLY H 344 " --> pdb=" O PHE H 379 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N PHE H 379 " --> pdb=" O GLY H 344 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N SER H 380 " --> pdb=" O GLU H 373 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N GLU H 373 " --> pdb=" O SER H 380 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'H' and resid 359 through 360 removed outlier: 3.500A pdb=" N LYS H 414 " --> pdb=" O CYS H 400 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'J' and resid 78 through 83 Processing sheet with id=AE8, first strand: chain 'J' and resid 115 through 118 removed outlier: 3.646A pdb=" N ILE J 126 " --> pdb=" O PHE J 115 " (cutoff:3.500A) 551 hydrogen bonds defined for protein. 1353 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: 6.81 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 14133 1.02 - 1.22: 43 1.22 - 1.42: 6057 1.42 - 1.62: 8950 1.62 - 1.81: 52 Bond restraints: 29235 Sorted by residual: bond pdb=" ND2 ASN G 230 " pdb="HD21 ASN G 230 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" ND2 ASN D 230 " pdb="HD21 ASN D 230 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" ND2 ASN B 230 " pdb="HD21 ASN B 230 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" NE ARG J 51 " pdb=" HE ARG J 51 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" NE2 GLN E 229 " pdb="HE22 GLN E 229 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.64e+01 ... (remaining 29230 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 51580 1.41 - 2.83: 1083 2.83 - 4.24: 120 4.24 - 5.65: 34 5.65 - 7.06: 9 Bond angle restraints: 52826 Sorted by residual: angle pdb=" N LYS A 414 " pdb=" CA LYS A 414 " pdb=" C LYS A 414 " ideal model delta sigma weight residual 109.50 103.87 5.63 1.58e+00 4.01e-01 1.27e+01 angle pdb=" CA ASP C 434 " pdb=" CB ASP C 434 " pdb=" CG ASP C 434 " ideal model delta sigma weight residual 112.60 109.36 3.24 1.00e+00 1.00e+00 1.05e+01 angle pdb=" N GLY A 421 " pdb=" CA GLY A 421 " pdb=" C GLY A 421 " ideal model delta sigma weight residual 113.18 106.46 6.72 2.37e+00 1.78e-01 8.05e+00 angle pdb=" N SER A 415 " pdb=" CA SER A 415 " pdb=" C SER A 415 " ideal model delta sigma weight residual 109.24 112.82 -3.58 1.51e+00 4.39e-01 5.61e+00 angle pdb=" CA ARG J 49 " pdb=" CB ARG J 49 " pdb=" CG ARG J 49 " ideal model delta sigma weight residual 114.10 109.41 4.69 2.00e+00 2.50e-01 5.50e+00 ... (remaining 52821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.29: 13547 21.29 - 42.58: 532 42.58 - 63.87: 125 63.87 - 85.16: 43 85.16 - 106.45: 25 Dihedral angle restraints: 14272 sinusoidal: 7995 harmonic: 6277 Sorted by residual: dihedral pdb=" O4 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C5 BMA Q 3 " pdb=" O5 BMA Q 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.74 106.45 1 3.00e+01 1.11e-03 1.37e+01 dihedral pdb=" O4 BMA L 3 " pdb=" C4 BMA L 3 " pdb=" C5 BMA L 3 " pdb=" O5 BMA L 3 " ideal model delta sinusoidal sigma weight residual -71.29 -177.23 105.94 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" O4 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C5 BMA K 3 " pdb=" O5 BMA K 3 " ideal model delta sinusoidal sigma weight residual -71.29 -176.82 105.53 1 3.00e+01 1.11e-03 1.35e+01 ... (remaining 14269 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2060 0.056 - 0.111: 340 0.111 - 0.167: 47 0.167 - 0.223: 1 0.223 - 0.278: 6 Chirality restraints: 2454 Sorted by residual: chirality pdb=" C5 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C6 BMA P 3 " pdb=" O5 BMA P 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" C5 BMA K 3 " pdb=" C4 BMA K 3 " pdb=" C6 BMA K 3 " pdb=" O5 BMA K 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 2451 not shown) Planarity restraints: 4450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D 357 " -0.095 2.00e-02 2.50e+03 1.03e-01 1.58e+02 pdb=" CD GLN D 357 " 0.007 2.00e-02 2.50e+03 pdb=" OE1 GLN D 357 " 0.090 2.00e-02 2.50e+03 pdb=" NE2 GLN D 357 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN D 357 " 0.151 2.00e-02 2.50e+03 pdb="HE22 GLN D 357 " -0.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN D 356 " 0.016 2.00e-02 2.50e+03 1.74e-02 4.52e+00 pdb=" CD GLN D 356 " -0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN D 356 " -0.015 2.00e-02 2.50e+03 pdb=" NE2 GLN D 356 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN D 356 " -0.025 2.00e-02 2.50e+03 pdb="HE22 GLN D 356 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 370 " -0.030 5.00e-02 4.00e+02 4.58e-02 3.35e+00 pdb=" N PRO A 371 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 371 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 371 " -0.026 5.00e-02 4.00e+02 ... (remaining 4447 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 1122 2.15 - 2.77: 57703 2.77 - 3.38: 80876 3.38 - 3.99: 105222 3.99 - 4.60: 159273 Nonbonded interactions: 404196 Sorted by model distance: nonbonded pdb=" OD1 ASP F 417 " pdb=" H THR F 420 " model vdw 1.542 2.450 nonbonded pdb="HH11 ARG J 51 " pdb=" O SER J 59 " model vdw 1.548 2.450 nonbonded pdb=" O LEU E 225 " pdb="HE22 GLN E 229 " model vdw 1.571 2.450 nonbonded pdb=" OE1 GLU B 328 " pdb=" H GLU B 328 " model vdw 1.579 2.450 nonbonded pdb=" OE1 GLU B 298 " pdb=" H GLU B 298 " model vdw 1.581 2.450 ... (remaining 404191 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 213 through 229 or (resid 230 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name ND2 or name H or name H \ A or name HB2 or name HB3 or name HD21)) or resid 231 through 279 or (resid 280 \ and (name N or name CA or name C or name O or name CB or name SG or name H or na \ me HA or name HB2 or name HB3)) or resid 281 through 432)) selection = (chain 'B' and resid 213 through 432) selection = (chain 'C' and (resid 213 through 279 or (resid 280 and (name N or name CA or na \ me C or name O or name CB or name SG or name H or name HA or name HB2 or name HB \ 3)) or resid 281 through 432)) selection = (chain 'D' and (resid 213 through 279 or (resid 280 and (name N or name CA or na \ me C or name O or name CB or name SG or name H or name HA or name HB2 or name HB \ 3)) or resid 281 through 432)) selection = (chain 'E' and resid 213 through 432) selection = (chain 'F' and (resid 213 through 279 or (resid 280 and (name N or name CA or na \ me C or name O or name CB or name SG or name H or name HA or name HB2 or name HB \ 3)) or resid 281 through 432)) selection = (chain 'G' and (resid 213 through 279 or (resid 280 and (name N or name CA or na \ me C or name O or name CB or name SG or name H or name HA or name HB2 or name HB \ 3)) or resid 281 through 432)) selection = (chain 'H' and (resid 213 through 229 or (resid 230 and (name N or name CA or na \ me C or name O or name CB or name CG or name OD1 or name ND2 or name H or name H \ A or name HB2 or name HB3 or name HD21)) or resid 231 through 279 or (resid 280 \ and (name N or name CA or name C or name O or name CB or name SG or name H or na \ me HA or name HB2 or name HB3)) or resid 281 through 432)) } ncs_group { reference = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 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: 0.180 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.610 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 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 : 0.004 0.045 15100 Z= 0.177 Angle : 0.574 8.013 20656 Z= 0.274 Chirality : 0.046 0.278 2454 Planarity : 0.004 0.046 2656 Dihedral : 13.605 106.451 5742 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.20), residues: 1899 helix: -1.33 (0.34), residues: 216 sheet: -0.94 (0.19), residues: 789 loop : -1.18 (0.21), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 359 TYR 0.007 0.001 TYR B 226 PHE 0.007 0.001 PHE B 369 TRP 0.006 0.001 TRP D 354 HIS 0.003 0.001 HIS J 120 Details of bonding type rmsd covalent geometry : bond 0.00359 (15059) covalent geometry : angle 0.55984 (20554) SS BOND : bond 0.00160 ( 21) SS BOND : angle 0.72185 ( 42) hydrogen bonds : bond 0.28412 ( 512) hydrogen bonds : angle 10.77844 ( 1353) link_BETA1-4 : bond 0.00693 ( 13) link_BETA1-4 : angle 1.85217 ( 39) link_NAG-ASN : bond 0.00358 ( 7) link_NAG-ASN : angle 3.18844 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 419 SER cc_start: 0.8971 (m) cc_final: 0.8651 (t) REVERT: F 310 ASP cc_start: 0.7826 (p0) cc_final: 0.7499 (p0) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.4127 time to fit residues: 51.9727 Evaluate side-chains 54 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN B 264 GLN B 266 GLN C 264 GLN C 285 ASN C 357 GLN C 393 GLN D 264 GLN ** E 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 ASN G 264 GLN ** G 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 264 GLN J 52 GLN J 91 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.070335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.049181 restraints weight = 180540.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.051700 restraints weight = 73235.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.053359 restraints weight = 43734.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.054385 restraints weight = 31974.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.055020 restraints weight = 26476.826| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15100 Z= 0.188 Angle : 0.608 6.532 20656 Z= 0.316 Chirality : 0.046 0.175 2454 Planarity : 0.005 0.060 2656 Dihedral : 9.484 63.716 2422 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 0.25 % Allowed : 6.31 % Favored : 93.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.19), residues: 1899 helix: -1.65 (0.32), residues: 223 sheet: -1.17 (0.18), residues: 830 loop : -1.39 (0.21), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 394 TYR 0.010 0.001 TYR A 226 PHE 0.011 0.001 PHE D 411 TRP 0.007 0.001 TRP F 392 HIS 0.005 0.001 HIS H 404 Details of bonding type rmsd covalent geometry : bond 0.00401 (15059) covalent geometry : angle 0.59575 (20554) SS BOND : bond 0.00389 ( 21) SS BOND : angle 0.84587 ( 42) hydrogen bonds : bond 0.05835 ( 512) hydrogen bonds : angle 7.96222 ( 1353) link_BETA1-4 : bond 0.00273 ( 13) link_BETA1-4 : angle 2.17970 ( 39) link_NAG-ASN : bond 0.00575 ( 7) link_NAG-ASN : angle 2.50033 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 310 ASP cc_start: 0.7836 (p0) cc_final: 0.7386 (p0) outliers start: 4 outliers final: 3 residues processed: 61 average time/residue: 0.3956 time to fit residues: 31.9601 Evaluate side-chains 55 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 131 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 113 optimal weight: 10.0000 chunk 116 optimal weight: 0.8980 chunk 183 optimal weight: 0.6980 chunk 110 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 10 optimal weight: 0.0370 chunk 115 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 GLN E 229 GLN E 264 GLN G 266 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.071849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.050434 restraints weight = 210574.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.053103 restraints weight = 90488.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.054812 restraints weight = 56779.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.055833 restraints weight = 43249.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.056364 restraints weight = 36735.228| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15100 Z= 0.115 Angle : 0.532 5.455 20656 Z= 0.269 Chirality : 0.044 0.180 2454 Planarity : 0.004 0.068 2656 Dihedral : 5.370 26.733 2422 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.43 % Allowed : 7.11 % Favored : 92.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.19), residues: 1899 helix: -1.42 (0.32), residues: 224 sheet: -1.14 (0.18), residues: 825 loop : -1.33 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 250 TYR 0.008 0.001 TYR A 321 PHE 0.008 0.001 PHE H 379 TRP 0.007 0.001 TRP A 354 HIS 0.004 0.001 HIS H 404 Details of bonding type rmsd covalent geometry : bond 0.00258 (15059) covalent geometry : angle 0.52021 (20554) SS BOND : bond 0.00285 ( 21) SS BOND : angle 0.74637 ( 42) hydrogen bonds : bond 0.04408 ( 512) hydrogen bonds : angle 6.95606 ( 1353) link_BETA1-4 : bond 0.00389 ( 13) link_BETA1-4 : angle 1.96045 ( 39) link_NAG-ASN : bond 0.00252 ( 7) link_NAG-ASN : angle 2.21127 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 310 ASP cc_start: 0.7810 (p0) cc_final: 0.7368 (p0) REVERT: G 257 ASP cc_start: 0.7860 (t0) cc_final: 0.7621 (t0) outliers start: 7 outliers final: 6 residues processed: 66 average time/residue: 0.3940 time to fit residues: 35.0159 Evaluate side-chains 59 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain G residue 280 CYS Chi-restraints excluded: chain H residue 349 ASP Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 131 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 16 optimal weight: 1.9990 chunk 167 optimal weight: 8.9990 chunk 169 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 11 optimal weight: 0.0000 chunk 99 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 54 optimal weight: 0.0370 chunk 47 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 overall best weight: 0.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 266 GLN G 266 GLN G 372 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.071546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.050109 restraints weight = 208872.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.052756 restraints weight = 90316.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.054447 restraints weight = 56914.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.055382 restraints weight = 43444.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.056051 restraints weight = 37184.882| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15100 Z= 0.121 Angle : 0.511 6.169 20656 Z= 0.260 Chirality : 0.043 0.169 2454 Planarity : 0.004 0.046 2656 Dihedral : 4.595 24.399 2422 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 0.49 % Allowed : 7.97 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.19), residues: 1899 helix: -1.29 (0.33), residues: 226 sheet: -1.13 (0.18), residues: 828 loop : -1.31 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 10 TYR 0.008 0.001 TYR E 321 PHE 0.013 0.001 PHE G 290 TRP 0.009 0.001 TRP A 354 HIS 0.003 0.001 HIS H 404 Details of bonding type rmsd covalent geometry : bond 0.00271 (15059) covalent geometry : angle 0.50131 (20554) SS BOND : bond 0.00238 ( 21) SS BOND : angle 0.58305 ( 42) hydrogen bonds : bond 0.03602 ( 512) hydrogen bonds : angle 6.52582 ( 1353) link_BETA1-4 : bond 0.00222 ( 13) link_BETA1-4 : angle 1.67020 ( 39) link_NAG-ASN : bond 0.00318 ( 7) link_NAG-ASN : angle 2.30906 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 310 ASP cc_start: 0.7785 (p0) cc_final: 0.7336 (p0) REVERT: G 257 ASP cc_start: 0.7860 (t0) cc_final: 0.7564 (t0) outliers start: 8 outliers final: 6 residues processed: 63 average time/residue: 0.3946 time to fit residues: 33.4593 Evaluate side-chains 58 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 131 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 92 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 146 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 144 optimal weight: 3.9990 chunk 140 optimal weight: 9.9990 chunk 123 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 266 GLN H 266 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.070637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.049169 restraints weight = 211093.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.051732 restraints weight = 91973.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.053356 restraints weight = 58290.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.054397 restraints weight = 44770.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.054910 restraints weight = 38030.305| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15100 Z= 0.170 Angle : 0.526 6.531 20656 Z= 0.268 Chirality : 0.042 0.170 2454 Planarity : 0.004 0.046 2656 Dihedral : 4.526 25.213 2422 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.61 % Allowed : 9.01 % Favored : 90.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.19), residues: 1899 helix: -1.42 (0.33), residues: 226 sheet: -1.20 (0.18), residues: 829 loop : -1.42 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 250 TYR 0.011 0.001 TYR E 321 PHE 0.010 0.001 PHE C 369 TRP 0.013 0.001 TRP A 354 HIS 0.003 0.001 HIS H 404 Details of bonding type rmsd covalent geometry : bond 0.00367 (15059) covalent geometry : angle 0.51655 (20554) SS BOND : bond 0.00232 ( 21) SS BOND : angle 0.64139 ( 42) hydrogen bonds : bond 0.03604 ( 512) hydrogen bonds : angle 6.40339 ( 1353) link_BETA1-4 : bond 0.00235 ( 13) link_BETA1-4 : angle 1.51455 ( 39) link_NAG-ASN : bond 0.00467 ( 7) link_NAG-ASN : angle 2.44868 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 310 ASP cc_start: 0.7800 (p0) cc_final: 0.7360 (p0) REVERT: G 257 ASP cc_start: 0.7947 (t0) cc_final: 0.7683 (t0) outliers start: 10 outliers final: 8 residues processed: 62 average time/residue: 0.3748 time to fit residues: 31.6812 Evaluate side-chains 57 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain H residue 349 ASP Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 131 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 100 optimal weight: 3.9990 chunk 74 optimal weight: 0.0970 chunk 128 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 0.0770 chunk 33 optimal weight: 0.2980 chunk 118 optimal weight: 20.0000 chunk 176 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 76 optimal weight: 0.3980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 264 GLN D 266 GLN H 266 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.071396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.049895 restraints weight = 209376.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.052524 restraints weight = 90559.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.054204 restraints weight = 57136.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.055248 restraints weight = 43619.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.055732 restraints weight = 37037.341| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15100 Z= 0.103 Angle : 0.507 7.244 20656 Z= 0.255 Chirality : 0.043 0.177 2454 Planarity : 0.004 0.048 2656 Dihedral : 4.372 24.218 2422 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.67 % Allowed : 9.07 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.19), residues: 1899 helix: -1.22 (0.33), residues: 225 sheet: -1.09 (0.18), residues: 828 loop : -1.32 (0.22), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 394 TYR 0.007 0.001 TYR E 321 PHE 0.010 0.001 PHE C 246 TRP 0.012 0.001 TRP A 354 HIS 0.004 0.001 HIS H 404 Details of bonding type rmsd covalent geometry : bond 0.00237 (15059) covalent geometry : angle 0.49936 (20554) SS BOND : bond 0.00195 ( 21) SS BOND : angle 0.47055 ( 42) hydrogen bonds : bond 0.03267 ( 512) hydrogen bonds : angle 6.12315 ( 1353) link_BETA1-4 : bond 0.00262 ( 13) link_BETA1-4 : angle 1.38610 ( 39) link_NAG-ASN : bond 0.00266 ( 7) link_NAG-ASN : angle 2.22701 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 310 ASP cc_start: 0.7807 (p0) cc_final: 0.7363 (p0) REVERT: G 257 ASP cc_start: 0.7883 (t0) cc_final: 0.7587 (t0) outliers start: 11 outliers final: 9 residues processed: 61 average time/residue: 0.3709 time to fit residues: 30.7049 Evaluate side-chains 60 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain G residue 280 CYS Chi-restraints excluded: chain H residue 349 ASP Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 131 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 141 optimal weight: 4.9990 chunk 140 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 44 optimal weight: 9.9990 chunk 185 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 160 optimal weight: 0.5980 chunk 158 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.071301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.049807 restraints weight = 209675.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.052423 restraints weight = 90819.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.054112 restraints weight = 57454.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.055141 restraints weight = 43801.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.055642 restraints weight = 37356.715| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 15100 Z= 0.110 Angle : 0.501 6.048 20656 Z= 0.252 Chirality : 0.043 0.172 2454 Planarity : 0.004 0.049 2656 Dihedral : 4.242 22.809 2422 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 0.67 % Allowed : 9.62 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.19), residues: 1899 helix: -1.13 (0.33), residues: 224 sheet: -1.05 (0.18), residues: 827 loop : -1.31 (0.22), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 250 TYR 0.008 0.001 TYR E 321 PHE 0.008 0.001 PHE C 246 TRP 0.011 0.001 TRP A 354 HIS 0.004 0.001 HIS H 404 Details of bonding type rmsd covalent geometry : bond 0.00250 (15059) covalent geometry : angle 0.49256 (20554) SS BOND : bond 0.00174 ( 21) SS BOND : angle 0.44935 ( 42) hydrogen bonds : bond 0.03128 ( 512) hydrogen bonds : angle 5.91490 ( 1353) link_BETA1-4 : bond 0.00247 ( 13) link_BETA1-4 : angle 1.36593 ( 39) link_NAG-ASN : bond 0.00301 ( 7) link_NAG-ASN : angle 2.25000 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 310 ASP cc_start: 0.7803 (p0) cc_final: 0.7352 (p0) REVERT: G 257 ASP cc_start: 0.7887 (t0) cc_final: 0.7589 (t0) REVERT: G 430 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8476 (t) outliers start: 11 outliers final: 9 residues processed: 62 average time/residue: 0.3718 time to fit residues: 31.7355 Evaluate side-chains 59 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain G residue 280 CYS Chi-restraints excluded: chain G residue 430 VAL Chi-restraints excluded: chain H residue 349 ASP Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 131 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 147 optimal weight: 1.9990 chunk 168 optimal weight: 0.8980 chunk 159 optimal weight: 9.9990 chunk 68 optimal weight: 3.9990 chunk 176 optimal weight: 3.9990 chunk 21 optimal weight: 0.0770 chunk 87 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.070983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.049483 restraints weight = 210334.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.052070 restraints weight = 91461.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.053751 restraints weight = 57934.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.054740 restraints weight = 44271.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.055243 restraints weight = 37838.516| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15100 Z= 0.129 Angle : 0.502 6.269 20656 Z= 0.254 Chirality : 0.042 0.172 2454 Planarity : 0.004 0.048 2656 Dihedral : 4.219 23.898 2422 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 0.61 % Allowed : 9.80 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.19), residues: 1899 helix: -1.11 (0.33), residues: 224 sheet: -1.09 (0.18), residues: 833 loop : -1.29 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 394 TYR 0.008 0.001 TYR E 321 PHE 0.008 0.001 PHE C 246 TRP 0.015 0.001 TRP A 354 HIS 0.004 0.001 HIS H 404 Details of bonding type rmsd covalent geometry : bond 0.00288 (15059) covalent geometry : angle 0.49369 (20554) SS BOND : bond 0.00182 ( 21) SS BOND : angle 0.50207 ( 42) hydrogen bonds : bond 0.03078 ( 512) hydrogen bonds : angle 5.79680 ( 1353) link_BETA1-4 : bond 0.00227 ( 13) link_BETA1-4 : angle 1.38090 ( 39) link_NAG-ASN : bond 0.00383 ( 7) link_NAG-ASN : angle 2.30424 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 310 ASP cc_start: 0.7808 (p0) cc_final: 0.7386 (p0) REVERT: G 257 ASP cc_start: 0.7965 (t0) cc_final: 0.7680 (t0) REVERT: G 430 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8456 (t) outliers start: 10 outliers final: 9 residues processed: 57 average time/residue: 0.3842 time to fit residues: 30.1713 Evaluate side-chains 57 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain G residue 280 CYS Chi-restraints excluded: chain G residue 430 VAL Chi-restraints excluded: chain H residue 349 ASP Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 131 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 5 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 53 optimal weight: 9.9990 chunk 131 optimal weight: 0.0010 chunk 139 optimal weight: 0.8980 chunk 114 optimal weight: 10.0000 chunk 77 optimal weight: 0.0570 chunk 176 optimal weight: 3.9990 overall best weight: 0.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.071475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.049980 restraints weight = 208893.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.052628 restraints weight = 90610.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.054315 restraints weight = 57150.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.055282 restraints weight = 43615.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.055966 restraints weight = 37244.395| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15100 Z= 0.095 Angle : 0.492 5.837 20656 Z= 0.248 Chirality : 0.043 0.176 2454 Planarity : 0.004 0.050 2656 Dihedral : 4.122 22.400 2422 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.49 % Allowed : 10.05 % Favored : 89.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.19), residues: 1899 helix: -0.96 (0.33), residues: 224 sheet: -0.99 (0.18), residues: 833 loop : -1.21 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 394 TYR 0.006 0.001 TYR A 321 PHE 0.007 0.001 PHE H 379 TRP 0.012 0.001 TRP A 354 HIS 0.004 0.001 HIS H 404 Details of bonding type rmsd covalent geometry : bond 0.00219 (15059) covalent geometry : angle 0.48456 (20554) SS BOND : bond 0.00166 ( 21) SS BOND : angle 0.42889 ( 42) hydrogen bonds : bond 0.02912 ( 512) hydrogen bonds : angle 5.59661 ( 1353) link_BETA1-4 : bond 0.00264 ( 13) link_BETA1-4 : angle 1.31006 ( 39) link_NAG-ASN : bond 0.00241 ( 7) link_NAG-ASN : angle 2.14645 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 310 ASP cc_start: 0.7777 (p0) cc_final: 0.7361 (p0) REVERT: G 257 ASP cc_start: 0.7978 (t0) cc_final: 0.7690 (t0) REVERT: G 430 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8401 (t) REVERT: J 67 TYR cc_start: 0.8390 (m-80) cc_final: 0.8036 (m-80) outliers start: 8 outliers final: 7 residues processed: 61 average time/residue: 0.3489 time to fit residues: 29.3696 Evaluate side-chains 58 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain G residue 280 CYS Chi-restraints excluded: chain G residue 430 VAL Chi-restraints excluded: chain H residue 349 ASP Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 131 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 77 optimal weight: 0.0570 chunk 24 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 122 optimal weight: 0.4980 chunk 169 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 127 optimal weight: 0.0980 chunk 162 optimal weight: 9.9990 chunk 176 optimal weight: 3.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.070770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.049249 restraints weight = 209033.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.051811 restraints weight = 91722.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.053475 restraints weight = 58287.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.054366 restraints weight = 44620.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.055050 restraints weight = 38457.172| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15100 Z= 0.141 Angle : 0.509 6.376 20656 Z= 0.257 Chirality : 0.042 0.168 2454 Planarity : 0.004 0.048 2656 Dihedral : 4.146 23.663 2422 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.61 % Allowed : 10.23 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.19), residues: 1899 helix: -1.04 (0.34), residues: 224 sheet: -1.03 (0.18), residues: 834 loop : -1.28 (0.22), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 394 TYR 0.009 0.001 TYR E 321 PHE 0.010 0.001 PHE A 369 TRP 0.016 0.001 TRP A 354 HIS 0.004 0.001 HIS H 404 Details of bonding type rmsd covalent geometry : bond 0.00313 (15059) covalent geometry : angle 0.50060 (20554) SS BOND : bond 0.00176 ( 21) SS BOND : angle 0.50175 ( 42) hydrogen bonds : bond 0.02973 ( 512) hydrogen bonds : angle 5.62348 ( 1353) link_BETA1-4 : bond 0.00227 ( 13) link_BETA1-4 : angle 1.39916 ( 39) link_NAG-ASN : bond 0.00453 ( 7) link_NAG-ASN : angle 2.34499 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3798 Ramachandran restraints generated. 1899 Oldfield, 0 Emsley, 1899 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 310 ASP cc_start: 0.7757 (p0) cc_final: 0.7325 (p0) REVERT: G 257 ASP cc_start: 0.8002 (t0) cc_final: 0.7746 (t0) REVERT: G 430 VAL cc_start: 0.8616 (OUTLIER) cc_final: 0.8405 (t) outliers start: 10 outliers final: 9 residues processed: 55 average time/residue: 0.3658 time to fit residues: 27.8266 Evaluate side-chains 57 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 358 ASP Chi-restraints excluded: chain E residue 277 LEU Chi-restraints excluded: chain E residue 350 ILE Chi-restraints excluded: chain G residue 280 CYS Chi-restraints excluded: chain G residue 430 VAL Chi-restraints excluded: chain H residue 349 ASP Chi-restraints excluded: chain J residue 32 ASN Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 131 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 185 optimal weight: 0.0970 chunk 171 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 chunk 180 optimal weight: 1.9990 chunk 152 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 178 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.071455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.049904 restraints weight = 209892.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.052550 restraints weight = 91114.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.054259 restraints weight = 57444.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.055268 restraints weight = 43760.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.055760 restraints weight = 37279.697| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15100 Z= 0.093 Angle : 0.491 5.846 20656 Z= 0.247 Chirality : 0.043 0.175 2454 Planarity : 0.004 0.050 2656 Dihedral : 4.077 22.671 2422 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.49 % Allowed : 10.23 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.19), residues: 1899 helix: -0.87 (0.34), residues: 224 sheet: -0.97 (0.18), residues: 833 loop : -1.18 (0.22), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 394 TYR 0.006 0.001 TYR A 321 PHE 0.008 0.001 PHE H 379 TRP 0.013 0.001 TRP A 354 HIS 0.004 0.001 HIS H 404 Details of bonding type rmsd covalent geometry : bond 0.00216 (15059) covalent geometry : angle 0.48387 (20554) SS BOND : bond 0.00155 ( 21) SS BOND : angle 0.39738 ( 42) hydrogen bonds : bond 0.02813 ( 512) hydrogen bonds : angle 5.45481 ( 1353) link_BETA1-4 : bond 0.00272 ( 13) link_BETA1-4 : angle 1.31259 ( 39) link_NAG-ASN : bond 0.00247 ( 7) link_NAG-ASN : angle 2.13758 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5448.90 seconds wall clock time: 93 minutes 19.60 seconds (5599.60 seconds total)