Starting phenix.real_space_refine on Wed Mar 4 03:14:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pqt_13604/03_2026/7pqt_13604.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pqt_13604/03_2026/7pqt_13604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7pqt_13604/03_2026/7pqt_13604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pqt_13604/03_2026/7pqt_13604.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pqt_13604/03_2026/7pqt_13604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pqt_13604/03_2026/7pqt_13604.map" } resolution = 2.65 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= 0.002 sd= 0.040 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 K 4 8.98 5 S 68 5.16 5 C 6876 2.51 5 N 1732 2.21 5 O 1784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10464 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2613 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 318, 2575 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 318, 2575 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 5 bond proxies already assigned to first conformer: 2608 Chain: "B" Number of atoms: 2613 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 318, 2575 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 318, 2575 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 5 bond proxies already assigned to first conformer: 2608 Chain: "C" Number of atoms: 2613 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 318, 2575 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 318, 2575 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 5 bond proxies already assigned to first conformer: 2608 Chain: "D" Number of atoms: 2613 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 318, 2575 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 318, 2575 Classifications: {'peptide': 318} Link IDs: {'PTRANS': 14, 'TRANS': 303} Chain breaks: 5 bond proxies already assigned to first conformer: 2608 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 16 residue: pdb=" N AARG A 113 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 113 " occ=0.50 residue: pdb=" N ATHR A 241 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR A 241 " occ=0.50 residue: pdb=" N AARG A 368 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 368 " occ=0.50 residue: pdb=" N ALYS A 449 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 449 " occ=0.50 residue: pdb=" N AARG B 113 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 113 " occ=0.50 residue: pdb=" N ATHR B 241 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR B 241 " occ=0.50 residue: pdb=" N AARG B 368 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 368 " occ=0.50 residue: pdb=" N ALYS B 449 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 449 " occ=0.50 residue: pdb=" N AARG C 113 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 113 " occ=0.50 residue: pdb=" N ATHR C 241 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR C 241 " occ=0.50 residue: pdb=" N AARG C 368 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 368 " occ=0.50 residue: pdb=" N ALYS C 449 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS C 449 " occ=0.50 ... (remaining 4 not shown) Time building chain proxies: 4.47, per 1000 atoms: 0.43 Number of scatterers: 10464 At special positions: 0 Unit cell: (118.9, 119.72, 113.98, 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) K 4 19.00 S 68 16.00 O 1784 8.00 N 1732 7.00 C 6876 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.86 Conformation dependent library (CDL) restraints added in 922.8 milliseconds 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 4 sheets defined 61.6% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 33 through 38 removed outlier: 3.597A pdb=" N ALA A 38 " --> pdb=" O ALA A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 45 Processing helix chain 'A' and resid 63 through 73 removed outlier: 3.962A pdb=" N TYR A 70 " --> pdb=" O HIS A 66 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TYR A 71 " --> pdb=" O ILE A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 105 through 117 removed outlier: 5.410A pdb=" N HIS A 112 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N AARG A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 210 removed outlier: 3.579A pdb=" N PHE A 198 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N PHE A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 257 Processing helix chain 'A' and resid 286 through 292 removed outlier: 4.144A pdb=" N TYR A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 319 Processing helix chain 'A' and resid 320 through 326 removed outlier: 3.767A pdb=" N LEU A 324 " --> pdb=" O ARG A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 338 Processing helix chain 'A' and resid 342 through 369 removed outlier: 3.529A pdb=" N LEU A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TYR A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ILE A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 399 removed outlier: 4.242A pdb=" N TRP A 392 " --> pdb=" O PRO A 388 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TRP A 393 " --> pdb=" O ILE A 389 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N THR A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 430 removed outlier: 3.636A pdb=" N LEU A 422 " --> pdb=" O ALA A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 450 removed outlier: 3.606A pdb=" N ASN A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE A 439 " --> pdb=" O ILE A 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 27 Processing helix chain 'B' and resid 33 through 37 Processing helix chain 'B' and resid 41 through 45 Processing helix chain 'B' and resid 63 through 73 removed outlier: 3.521A pdb=" N ILE B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N TYR B 70 " --> pdb=" O HIS B 66 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N TYR B 71 " --> pdb=" O ILE B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 105 through 117 removed outlier: 5.378A pdb=" N HIS B 112 " --> pdb=" O THR B 108 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N AARG B 113 " --> pdb=" O TYR B 109 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU B 117 " --> pdb=" O AARG B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 210 removed outlier: 3.569A pdb=" N PHE B 198 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N PHE B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 257 removed outlier: 3.623A pdb=" N THR B 257 " --> pdb=" O VAL B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 292 removed outlier: 4.359A pdb=" N TYR B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 318 removed outlier: 3.678A pdb=" N ILE B 318 " --> pdb=" O PHE B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 319 through 325 removed outlier: 4.066A pdb=" N LYS B 323 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 324 " --> pdb=" O ARG B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 338 removed outlier: 3.551A pdb=" N VAL B 333 " --> pdb=" O VAL B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 369 removed outlier: 3.563A pdb=" N LEU B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR B 365 " --> pdb=" O THR B 361 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE B 369 " --> pdb=" O TYR B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 399 removed outlier: 4.275A pdb=" N TRP B 392 " --> pdb=" O PRO B 388 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N TRP B 393 " --> pdb=" O ILE B 389 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR B 399 " --> pdb=" O VAL B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 430 removed outlier: 3.627A pdb=" N LEU B 422 " --> pdb=" O ALA B 418 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 450 removed outlier: 3.628A pdb=" N ASN B 438 " --> pdb=" O VAL B 434 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE B 439 " --> pdb=" O ILE B 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 33 through 37 Processing helix chain 'C' and resid 41 through 45 Processing helix chain 'C' and resid 63 through 73 removed outlier: 3.510A pdb=" N ILE C 67 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR C 70 " --> pdb=" O HIS C 66 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR C 71 " --> pdb=" O ILE C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 95 Processing helix chain 'C' and resid 105 through 117 removed outlier: 5.327A pdb=" N HIS C 112 " --> pdb=" O THR C 108 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N AARG C 113 " --> pdb=" O TYR C 109 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU C 117 " --> pdb=" O AARG C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 210 removed outlier: 3.895A pdb=" N PHE C 198 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N PHE C 199 " --> pdb=" O ALA C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 257 Processing helix chain 'C' and resid 287 through 292 Processing helix chain 'C' and resid 314 through 319 removed outlier: 3.875A pdb=" N ILE C 318 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 325 removed outlier: 3.905A pdb=" N LEU C 324 " --> pdb=" O ARG C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 338 Processing helix chain 'C' and resid 342 through 369 removed outlier: 3.526A pdb=" N TYR C 364 " --> pdb=" O ALA C 360 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR C 365 " --> pdb=" O THR C 361 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE C 369 " --> pdb=" O TYR C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 399 removed outlier: 4.320A pdb=" N TRP C 392 " --> pdb=" O PRO C 388 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP C 393 " --> pdb=" O ILE C 389 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR C 399 " --> pdb=" O VAL C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 430 removed outlier: 3.634A pdb=" N LEU C 422 " --> pdb=" O ALA C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 450 removed outlier: 3.594A pdb=" N ASN C 438 " --> pdb=" O VAL C 434 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE C 439 " --> pdb=" O ILE C 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 33 through 37 Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.899A pdb=" N PHE D 46 " --> pdb=" O HIS D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.955A pdb=" N TYR D 70 " --> pdb=" O HIS D 66 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR D 71 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 95 Processing helix chain 'D' and resid 105 through 117 removed outlier: 5.104A pdb=" N HIS D 112 " --> pdb=" O THR D 108 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N AARG D 113 " --> pdb=" O TYR D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 210 removed outlier: 3.723A pdb=" N PHE D 198 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N PHE D 199 " --> pdb=" O ALA D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 257 Processing helix chain 'D' and resid 287 through 292 Processing helix chain 'D' and resid 314 through 318 removed outlier: 4.004A pdb=" N ILE D 318 " --> pdb=" O PHE D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 319 through 325 removed outlier: 4.040A pdb=" N LYS D 323 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU D 324 " --> pdb=" O ARG D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 338 removed outlier: 3.517A pdb=" N VAL D 333 " --> pdb=" O VAL D 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 369 removed outlier: 3.522A pdb=" N LEU D 348 " --> pdb=" O GLU D 344 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR D 364 " --> pdb=" O ALA D 360 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TYR D 365 " --> pdb=" O THR D 361 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ILE D 369 " --> pdb=" O TYR D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 399 removed outlier: 4.311A pdb=" N TRP D 392 " --> pdb=" O PRO D 388 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TRP D 393 " --> pdb=" O ILE D 389 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N THR D 399 " --> pdb=" O VAL D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 410 through 430 removed outlier: 3.648A pdb=" N LEU D 422 " --> pdb=" O ALA D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 450 removed outlier: 3.604A pdb=" N ASN D 438 " --> pdb=" O VAL D 434 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE D 439 " --> pdb=" O ILE D 435 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 22 Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 22 Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 22 Processing sheet with id=AA4, first strand: chain 'D' and resid 17 through 22 512 hydrogen bonds defined for protein. 1457 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: 1.69 Time building geometry restraints manager: 1.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3165 1.34 - 1.45: 2304 1.45 - 1.57: 5195 1.57 - 1.69: 0 1.69 - 1.81: 104 Bond restraints: 10768 Sorted by residual: bond pdb=" CB THR D 361 " pdb=" CG2 THR D 361 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.93e+00 bond pdb=" CG ARG D 59 " pdb=" CD ARG D 59 " ideal model delta sigma weight residual 1.520 1.461 0.059 3.00e-02 1.11e+03 3.86e+00 bond pdb=" CB THR A 21 " pdb=" CG2 THR A 21 " ideal model delta sigma weight residual 1.521 1.464 0.057 3.30e-02 9.18e+02 3.01e+00 bond pdb=" C ALA D 38 " pdb=" N GLU D 39 " ideal model delta sigma weight residual 1.329 1.360 -0.031 1.86e-02 2.89e+03 2.85e+00 bond pdb=" CG LEU B 209 " pdb=" CD1 LEU B 209 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.83e+00 ... (remaining 10763 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 14003 1.84 - 3.67: 555 3.67 - 5.51: 74 5.51 - 7.35: 20 7.35 - 9.18: 4 Bond angle restraints: 14656 Sorted by residual: angle pdb=" C GLU D 242 " pdb=" N ALA D 243 " pdb=" CA ALA D 243 " ideal model delta sigma weight residual 122.08 116.20 5.88 1.53e+00 4.27e-01 1.48e+01 angle pdb=" C ARG A 72 " pdb=" N THR A 73 " pdb=" CA THR A 73 " ideal model delta sigma weight residual 121.54 114.23 7.31 1.91e+00 2.74e-01 1.46e+01 angle pdb=" C ARG C 72 " pdb=" N THR C 73 " pdb=" CA THR C 73 " ideal model delta sigma weight residual 121.54 114.59 6.95 1.91e+00 2.74e-01 1.32e+01 angle pdb=" C ARG B 72 " pdb=" N THR B 73 " pdb=" CA THR B 73 " ideal model delta sigma weight residual 121.54 114.80 6.74 1.91e+00 2.74e-01 1.25e+01 angle pdb=" C ARG D 72 " pdb=" N THR D 73 " pdb=" CA THR D 73 " ideal model delta sigma weight residual 121.54 114.98 6.56 1.91e+00 2.74e-01 1.18e+01 ... (remaining 14651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.05: 5199 18.05 - 36.09: 705 36.09 - 54.14: 209 54.14 - 72.18: 47 72.18 - 90.23: 12 Dihedral angle restraints: 6172 sinusoidal: 2420 harmonic: 3752 Sorted by residual: dihedral pdb=" CA GLU D 242 " pdb=" C GLU D 242 " pdb=" N ALA D 243 " pdb=" CA ALA D 243 " ideal model delta harmonic sigma weight residual -180.00 -155.84 -24.16 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" CA GLY B 74 " pdb=" C GLY B 74 " pdb=" N LYS B 75 " pdb=" CA LYS B 75 " ideal model delta harmonic sigma weight residual -180.00 -156.92 -23.08 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA VAL A 254 " pdb=" C VAL A 254 " pdb=" N TRP A 255 " pdb=" CA TRP A 255 " ideal model delta harmonic sigma weight residual 180.00 157.09 22.91 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 6169 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1028 0.048 - 0.096: 481 0.096 - 0.144: 100 0.144 - 0.192: 22 0.192 - 0.240: 1 Chirality restraints: 1632 Sorted by residual: chirality pdb=" CB ILE C 286 " pdb=" CA ILE C 286 " pdb=" CG1 ILE C 286 " pdb=" CG2 ILE C 286 " both_signs ideal model delta sigma weight residual False 2.64 2.88 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA MET D 430 " pdb=" N MET D 430 " pdb=" C MET D 430 " pdb=" CB MET D 430 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.16e-01 chirality pdb=" CA MET C 430 " pdb=" N MET C 430 " pdb=" C MET C 430 " pdb=" CB MET C 430 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.42e-01 ... (remaining 1629 not shown) Planarity restraints: 1828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 84 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.55e+00 pdb=" N PRO C 85 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 85 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 85 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 84 " -0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO B 85 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 85 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 85 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 84 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.22e+00 pdb=" N PRO A 85 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " -0.025 5.00e-02 4.00e+02 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.73: 1414 2.73 - 3.33: 11758 3.33 - 3.94: 19644 3.94 - 4.54: 28801 4.54 - 5.14: 42168 Nonbonded interactions: 103785 Sorted by model distance: nonbonded pdb=" OD2 ASP D 97 " pdb=" OG1 THR D 99 " model vdw 2.130 3.040 nonbonded pdb=" OD1 ASP B 97 " pdb=" OG1 THR B 99 " model vdw 2.166 3.040 nonbonded pdb=" OD1 ASP C 97 " pdb=" OG1 THR C 99 " model vdw 2.171 3.040 nonbonded pdb=" OE1 GLU C 98 " pdb=" OH TYR C 109 " model vdw 2.182 3.040 nonbonded pdb=" NH2 ARG B 33 " pdb=" O PHE B 93 " model vdw 2.191 3.120 ... (remaining 103780 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 7 through 112 or resid 114 through 240 or resid 242 throug \ h 367 or resid 369 through 448 or resid 450 through 453)) selection = (chain 'B' and (resid 7 through 112 or resid 114 through 240 or resid 242 throug \ h 367 or resid 369 through 448 or resid 450 through 453)) selection = (chain 'C' and (resid 7 through 112 or resid 114 through 240 or resid 242 throug \ h 367 or resid 369 through 448 or resid 450 through 453)) selection = (chain 'D' and (resid 7 through 112 or resid 114 through 240 or resid 242 throug \ h 367 or resid 369 through 448 or resid 450 through 453)) } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.950 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: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.890 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 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:8.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 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 : 0.011 0.065 10768 Z= 0.463 Angle : 0.866 9.185 14656 Z= 0.486 Chirality : 0.055 0.240 1632 Planarity : 0.006 0.047 1828 Dihedral : 18.505 90.227 3756 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.65 % Allowed : 6.94 % Favored : 92.40 % Rotamer: Outliers : 10.42 % Allowed : 26.81 % Favored : 62.77 % 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: -3.82 (0.19), residues: 1268 helix: -2.16 (0.14), residues: 792 sheet: -1.87 (0.50), residues: 40 loop : -3.06 (0.25), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 320 TYR 0.022 0.002 TYR C 22 PHE 0.025 0.002 PHE C 56 TRP 0.008 0.002 TRP A 393 HIS 0.006 0.001 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.01073 (10768) covalent geometry : angle 0.86647 (14656) hydrogen bonds : bond 0.17200 ( 512) hydrogen bonds : angle 5.93393 ( 1457) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 194 time to evaluate : 0.430 Fit side-chains REVERT: A 23 ARG cc_start: 0.7431 (OUTLIER) cc_final: 0.6997 (mtt180) REVERT: A 339 ARG cc_start: 0.4856 (OUTLIER) cc_final: 0.4553 (mpt180) REVERT: A 344 GLU cc_start: 0.8124 (mp0) cc_final: 0.7916 (mp0) REVERT: A 450 GLN cc_start: 0.7056 (OUTLIER) cc_final: 0.6658 (mt0) REVERT: B 23 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.7312 (mtt180) REVERT: B 210 GLU cc_start: 0.7097 (mp0) cc_final: 0.6544 (mp0) REVERT: B 249 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6370 (mt-10) REVERT: C 24 SER cc_start: 0.8238 (OUTLIER) cc_final: 0.7952 (p) REVERT: C 259 GLU cc_start: 0.6705 (tt0) cc_final: 0.6403 (tt0) REVERT: C 380 GLU cc_start: 0.3075 (OUTLIER) cc_final: 0.2552 (mp0) REVERT: C 386 ASN cc_start: 0.7558 (OUTLIER) cc_final: 0.6986 (p0) REVERT: D 53 ASP cc_start: 0.5448 (t0) cc_final: 0.5155 (t0) REVERT: D 386 ASN cc_start: 0.7581 (OUTLIER) cc_final: 0.7074 (p0) outliers start: 99 outliers final: 46 residues processed: 278 average time/residue: 0.4353 time to fit residues: 132.8483 Evaluate side-chains 233 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 178 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 204 ILE Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 339 ARG Chi-restraints excluded: chain A residue 342 THR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 23 ARG Chi-restraints excluded: chain B residue 49 ASP Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 253 VAL Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 399 THR Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 10 ILE Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 24 SER Chi-restraints excluded: chain C residue 108 THR Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 350 ILE Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 386 ASN Chi-restraints excluded: chain C residue 399 THR Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 104 CYS Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 204 ILE Chi-restraints excluded: chain D residue 253 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 328 PHE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 342 THR Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain D residue 386 ASN Chi-restraints excluded: chain D residue 399 THR Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 427 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.0020 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 65 optimal weight: 0.0020 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN A 327 HIS B 66 HIS D 45 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.130179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.098349 restraints weight = 88081.184| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 4.22 r_work: 0.3153 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10768 Z= 0.139 Angle : 0.720 14.388 14656 Z= 0.359 Chirality : 0.044 0.176 1632 Planarity : 0.005 0.047 1828 Dihedral : 8.008 57.038 1503 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.82 % Favored : 94.85 % Rotamer: Outliers : 6.52 % Allowed : 29.89 % Favored : 63.59 % 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: -1.81 (0.22), residues: 1268 helix: -0.69 (0.18), residues: 800 sheet: None (None), residues: 0 loop : -1.96 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 326 TYR 0.018 0.002 TYR C 22 PHE 0.023 0.002 PHE D 315 TRP 0.016 0.002 TRP D 106 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00315 (10768) covalent geometry : angle 0.72039 (14656) hydrogen bonds : bond 0.04592 ( 512) hydrogen bonds : angle 4.28629 ( 1457) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 207 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 54 GLU cc_start: 0.8166 (pt0) cc_final: 0.7935 (pt0) REVERT: A 450 GLN cc_start: 0.8506 (OUTLIER) cc_final: 0.8205 (mt0) REVERT: B 49 ASP cc_start: 0.7423 (m-30) cc_final: 0.7206 (m-30) REVERT: B 345 PHE cc_start: 0.8927 (m-80) cc_final: 0.8640 (m-80) REVERT: C 54 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7613 (pt0) REVERT: C 197 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7055 (tp) REVERT: C 210 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: C 380 GLU cc_start: 0.6670 (OUTLIER) cc_final: 0.6089 (mp0) REVERT: D 53 ASP cc_start: 0.6516 (t0) cc_final: 0.6288 (t0) outliers start: 56 outliers final: 19 residues processed: 242 average time/residue: 0.4631 time to fit residues: 122.6533 Evaluate side-chains 213 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain C residue 11 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 54 GLU Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 328 PHE Chi-restraints excluded: chain D residue 389 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 5 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 122 optimal weight: 0.3980 chunk 19 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 ASN C 13 ASN C 438 ASN D 45 HIS D 111 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.129367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.097850 restraints weight = 89829.448| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 4.53 r_work: 0.3132 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3130 r_free = 0.3130 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3130 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 : 0.004 0.042 10768 Z= 0.158 Angle : 0.727 14.761 14656 Z= 0.356 Chirality : 0.044 0.180 1632 Planarity : 0.005 0.043 1828 Dihedral : 6.586 58.605 1439 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.90 % Favored : 94.77 % Rotamer: Outliers : 6.25 % Allowed : 30.07 % Favored : 63.68 % 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: -1.10 (0.22), residues: 1268 helix: -0.09 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -1.70 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 263 TYR 0.022 0.002 TYR C 48 PHE 0.023 0.002 PHE A 260 TRP 0.020 0.002 TRP B 255 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00372 (10768) covalent geometry : angle 0.72715 (14656) hydrogen bonds : bond 0.04758 ( 512) hydrogen bonds : angle 4.20427 ( 1457) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 206 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8305 (OUTLIER) cc_final: 0.8033 (p) REVERT: A 54 GLU cc_start: 0.8175 (pt0) cc_final: 0.7912 (pt0) REVERT: A 450 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.8124 (mt0) REVERT: B 24 SER cc_start: 0.8538 (OUTLIER) cc_final: 0.8269 (p) REVERT: B 49 ASP cc_start: 0.7437 (m-30) cc_final: 0.7127 (m-30) REVERT: B 210 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7991 (mp0) REVERT: B 345 PHE cc_start: 0.8864 (m-80) cc_final: 0.8610 (m-80) REVERT: B 349 ILE cc_start: 0.9068 (mp) cc_final: 0.8839 (mp) REVERT: C 54 GLU cc_start: 0.7777 (pt0) cc_final: 0.7564 (pt0) REVERT: C 201 LEU cc_start: 0.8141 (mm) cc_final: 0.7858 (mm) REVERT: C 210 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7676 (mp0) REVERT: C 314 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6724 (ptp-110) REVERT: D 53 ASP cc_start: 0.6477 (t0) cc_final: 0.6248 (t0) outliers start: 53 outliers final: 26 residues processed: 236 average time/residue: 0.4338 time to fit residues: 112.6688 Evaluate side-chains 225 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 194 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 328 PHE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 389 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 84 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 109 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 0.0470 chunk 87 optimal weight: 0.5980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 ASN D 45 HIS D 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.130028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.098529 restraints weight = 97073.512| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 4.71 r_work: 0.3137 rms_B_bonded: 4.51 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10768 Z= 0.148 Angle : 0.720 14.531 14656 Z= 0.351 Chirality : 0.044 0.182 1632 Planarity : 0.005 0.043 1828 Dihedral : 6.214 52.973 1436 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.58 % Favored : 95.10 % Rotamer: Outliers : 6.61 % Allowed : 30.34 % Favored : 63.04 % 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: -0.73 (0.23), residues: 1268 helix: 0.18 (0.19), residues: 784 sheet: None (None), residues: 0 loop : -1.51 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 326 TYR 0.030 0.002 TYR C 48 PHE 0.020 0.001 PHE C 55 TRP 0.020 0.002 TRP B 255 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00344 (10768) covalent geometry : angle 0.71994 (14656) hydrogen bonds : bond 0.04486 ( 512) hydrogen bonds : angle 4.20139 ( 1457) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 201 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8281 (OUTLIER) cc_final: 0.8021 (p) REVERT: A 54 GLU cc_start: 0.8153 (pt0) cc_final: 0.7930 (pt0) REVERT: A 450 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8197 (mt0) REVERT: B 24 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.8245 (p) REVERT: B 49 ASP cc_start: 0.7392 (m-30) cc_final: 0.7072 (m-30) REVERT: B 345 PHE cc_start: 0.8879 (m-80) cc_final: 0.8594 (m-80) REVERT: B 349 ILE cc_start: 0.9015 (mp) cc_final: 0.8759 (mp) REVERT: C 54 GLU cc_start: 0.7808 (pt0) cc_final: 0.7483 (pt0) REVERT: C 201 LEU cc_start: 0.8137 (mm) cc_final: 0.7859 (mm) REVERT: C 210 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7644 (mp0) REVERT: C 314 ARG cc_start: 0.6976 (OUTLIER) cc_final: 0.6769 (ptp-110) REVERT: D 53 ASP cc_start: 0.6480 (t0) cc_final: 0.6251 (t0) REVERT: D 430 MET cc_start: 0.8818 (mmm) cc_final: 0.7873 (mtm) outliers start: 57 outliers final: 30 residues processed: 236 average time/residue: 0.4316 time to fit residues: 111.9219 Evaluate side-chains 226 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 191 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 328 PHE Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 35 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 107 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN D 45 HIS D 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.125950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.094189 restraints weight = 88252.942| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 4.11 r_work: 0.3090 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3090 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3090 r_free = 0.3090 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3090 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 10768 Z= 0.277 Angle : 0.764 13.208 14656 Z= 0.388 Chirality : 0.049 0.310 1632 Planarity : 0.006 0.051 1828 Dihedral : 6.407 51.332 1436 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.23 % Favored : 94.44 % Rotamer: Outliers : 6.61 % Allowed : 30.53 % Favored : 62.86 % 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: -0.71 (0.23), residues: 1268 helix: 0.20 (0.19), residues: 756 sheet: -0.40 (0.72), residues: 40 loop : -1.50 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 59 TYR 0.021 0.002 TYR C 22 PHE 0.026 0.002 PHE C 55 TRP 0.023 0.002 TRP D 255 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00656 (10768) covalent geometry : angle 0.76435 (14656) hydrogen bonds : bond 0.05744 ( 512) hydrogen bonds : angle 4.41207 ( 1457) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 191 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 54 GLU cc_start: 0.8266 (pt0) cc_final: 0.8049 (pt0) REVERT: A 89 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8095 (tt0) REVERT: A 450 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8164 (mt0) REVERT: B 24 SER cc_start: 0.8574 (OUTLIER) cc_final: 0.8226 (p) REVERT: B 49 ASP cc_start: 0.7529 (m-30) cc_final: 0.7249 (m-30) REVERT: B 54 GLU cc_start: 0.8041 (pt0) cc_final: 0.7811 (pt0) REVERT: B 89 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8123 (tt0) REVERT: B 349 ILE cc_start: 0.9076 (mp) cc_final: 0.8836 (mp) REVERT: C 210 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: D 24 SER cc_start: 0.8518 (OUTLIER) cc_final: 0.8204 (p) REVERT: D 53 ASP cc_start: 0.6539 (t0) cc_final: 0.6260 (t0) REVERT: D 213 GLU cc_start: 0.7929 (tp30) cc_final: 0.7505 (tp30) outliers start: 57 outliers final: 31 residues processed: 234 average time/residue: 0.4032 time to fit residues: 104.1255 Evaluate side-chains 227 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 24 SER Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 427 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 95 optimal weight: 0.0980 chunk 48 optimal weight: 0.0050 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 80 optimal weight: 0.1980 chunk 120 optimal weight: 0.9990 chunk 113 optimal weight: 0.1980 chunk 76 optimal weight: 0.9990 overall best weight: 0.2194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS B 111 GLN B 438 ASN C 112 HIS D 45 HIS D 111 GLN D 216 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.131966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.100276 restraints weight = 98095.864| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 4.70 r_work: 0.3172 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10768 Z= 0.123 Angle : 0.702 13.527 14656 Z= 0.339 Chirality : 0.042 0.160 1632 Planarity : 0.005 0.041 1828 Dihedral : 5.684 50.920 1433 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.17 % Favored : 95.51 % Rotamer: Outliers : 5.53 % Allowed : 31.25 % Favored : 63.22 % 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: -0.29 (0.23), residues: 1268 helix: 0.53 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -1.36 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 326 TYR 0.013 0.001 TYR C 22 PHE 0.021 0.001 PHE A 260 TRP 0.021 0.001 TRP B 255 HIS 0.004 0.001 HIS A 112 Details of bonding type rmsd covalent geometry : bond 0.00279 (10768) covalent geometry : angle 0.70234 (14656) hydrogen bonds : bond 0.03997 ( 512) hydrogen bonds : angle 4.13047 ( 1457) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 214 time to evaluate : 0.313 Fit side-chains revert: symmetry clash REVERT: A 54 GLU cc_start: 0.8105 (pt0) cc_final: 0.7902 (pt0) REVERT: A 89 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.8009 (tt0) REVERT: B 49 ASP cc_start: 0.7423 (m-30) cc_final: 0.7210 (m-30) REVERT: B 54 GLU cc_start: 0.7740 (pt0) cc_final: 0.7500 (pt0) REVERT: B 345 PHE cc_start: 0.8889 (m-80) cc_final: 0.8635 (m-80) REVERT: B 349 ILE cc_start: 0.9043 (mp) cc_final: 0.8812 (mp) REVERT: C 54 GLU cc_start: 0.7737 (pt0) cc_final: 0.7410 (pt0) REVERT: C 201 LEU cc_start: 0.8177 (mm) cc_final: 0.7897 (mm) REVERT: C 210 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7681 (mp0) REVERT: D 53 ASP cc_start: 0.6535 (t0) cc_final: 0.6297 (t0) REVERT: D 209 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8643 (OUTLIER) REVERT: D 213 GLU cc_start: 0.7946 (tp30) cc_final: 0.7481 (tp30) REVERT: D 430 MET cc_start: 0.8784 (mmm) cc_final: 0.7749 (mtm) outliers start: 45 outliers final: 22 residues processed: 241 average time/residue: 0.4221 time to fit residues: 111.9485 Evaluate side-chains 227 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 328 PHE Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 447 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 0 optimal weight: 4.9990 chunk 81 optimal weight: 0.9980 chunk 109 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 HIS D 45 HIS D 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.129008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.097528 restraints weight = 104687.436| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 4.60 r_work: 0.3122 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10768 Z= 0.198 Angle : 0.734 14.047 14656 Z= 0.360 Chirality : 0.045 0.180 1632 Planarity : 0.005 0.049 1828 Dihedral : 5.315 43.822 1427 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.66 % Favored : 95.02 % Rotamer: Outliers : 5.53 % Allowed : 31.88 % Favored : 62.59 % 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: -0.25 (0.23), residues: 1268 helix: 0.53 (0.20), residues: 760 sheet: -0.16 (0.72), residues: 40 loop : -1.23 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 314 TYR 0.017 0.001 TYR C 22 PHE 0.019 0.002 PHE C 55 TRP 0.025 0.002 TRP B 255 HIS 0.009 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00471 (10768) covalent geometry : angle 0.73366 (14656) hydrogen bonds : bond 0.04892 ( 512) hydrogen bonds : angle 4.21486 ( 1457) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8405 (OUTLIER) cc_final: 0.8135 (p) REVERT: B 49 ASP cc_start: 0.7643 (m-30) cc_final: 0.7413 (m-30) REVERT: B 349 ILE cc_start: 0.9130 (mp) cc_final: 0.8891 (mp) REVERT: C 201 LEU cc_start: 0.8401 (mm) cc_final: 0.8141 (mm) REVERT: C 210 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: D 53 ASP cc_start: 0.6656 (t0) cc_final: 0.6385 (t0) REVERT: D 430 MET cc_start: 0.8946 (mmm) cc_final: 0.7954 (mtm) outliers start: 45 outliers final: 31 residues processed: 223 average time/residue: 0.4303 time to fit residues: 105.2854 Evaluate side-chains 224 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 341 SER Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 10 ILE Chi-restraints excluded: chain D residue 213 GLU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 447 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 14 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 0.0670 chunk 19 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 77 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 102 optimal weight: 0.0770 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS C 327 HIS D 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.131136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.100310 restraints weight = 96185.984| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 4.75 r_work: 0.3158 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10768 Z= 0.141 Angle : 0.710 14.192 14656 Z= 0.345 Chirality : 0.043 0.172 1632 Planarity : 0.005 0.044 1828 Dihedral : 5.218 49.740 1427 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.25 % Favored : 95.42 % Rotamer: Outliers : 4.62 % Allowed : 32.52 % Favored : 62.86 % 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: -0.09 (0.23), residues: 1268 helix: 0.69 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -1.29 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 314 TYR 0.015 0.001 TYR C 22 PHE 0.015 0.001 PHE C 55 TRP 0.026 0.002 TRP B 255 HIS 0.007 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00332 (10768) covalent geometry : angle 0.71044 (14656) hydrogen bonds : bond 0.04345 ( 512) hydrogen bonds : angle 4.12440 ( 1457) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 193 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8323 (OUTLIER) cc_final: 0.8096 (p) REVERT: A 54 GLU cc_start: 0.8022 (pt0) cc_final: 0.7737 (pm20) REVERT: B 49 ASP cc_start: 0.7566 (m-30) cc_final: 0.7356 (m-30) REVERT: B 345 PHE cc_start: 0.8879 (m-80) cc_final: 0.8617 (m-80) REVERT: B 349 ILE cc_start: 0.9124 (mp) cc_final: 0.8876 (mp) REVERT: C 201 LEU cc_start: 0.8297 (mm) cc_final: 0.7977 (mm) REVERT: C 210 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.7735 (mp0) REVERT: D 53 ASP cc_start: 0.6629 (t0) cc_final: 0.6368 (t0) REVERT: D 209 LEU cc_start: 0.8924 (mp) cc_final: 0.8718 (OUTLIER) REVERT: D 430 MET cc_start: 0.8855 (mmm) cc_final: 0.7830 (mtm) outliers start: 35 outliers final: 22 residues processed: 218 average time/residue: 0.4223 time to fit residues: 101.3750 Evaluate side-chains 206 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 447 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 51 optimal weight: 0.4980 chunk 43 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 13 optimal weight: 0.0040 chunk 70 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS C 327 HIS D 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.130834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.099369 restraints weight = 87181.891| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 4.27 r_work: 0.3171 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10768 Z= 0.142 Angle : 0.715 14.452 14656 Z= 0.344 Chirality : 0.043 0.170 1632 Planarity : 0.005 0.042 1828 Dihedral : 5.144 55.688 1426 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.74 % Favored : 94.93 % Rotamer: Outliers : 4.35 % Allowed : 33.06 % Favored : 62.59 % 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: 0.01 (0.24), residues: 1268 helix: 0.78 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.27 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 314 TYR 0.015 0.001 TYR C 22 PHE 0.019 0.002 PHE A 256 TRP 0.027 0.002 TRP B 255 HIS 0.006 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00335 (10768) covalent geometry : angle 0.71462 (14656) hydrogen bonds : bond 0.04302 ( 512) hydrogen bonds : angle 4.08506 ( 1457) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 190 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8332 (OUTLIER) cc_final: 0.8106 (p) REVERT: B 345 PHE cc_start: 0.8868 (m-80) cc_final: 0.8606 (m-80) REVERT: B 349 ILE cc_start: 0.9122 (mp) cc_final: 0.8882 (mp) REVERT: C 111 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8396 (tm-30) REVERT: C 201 LEU cc_start: 0.8313 (mm) cc_final: 0.8009 (mm) REVERT: C 210 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: D 53 ASP cc_start: 0.6625 (t0) cc_final: 0.6363 (t0) REVERT: D 430 MET cc_start: 0.8833 (mmm) cc_final: 0.7814 (mtm) outliers start: 32 outliers final: 25 residues processed: 211 average time/residue: 0.4239 time to fit residues: 98.6361 Evaluate side-chains 211 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 183 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 315 PHE Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 447 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 22 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 37 optimal weight: 0.3980 chunk 119 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS C 327 HIS D 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.131190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.099660 restraints weight = 82610.761| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 4.00 r_work: 0.3175 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.381 10768 Z= 0.291 Angle : 1.133 69.287 14656 Z= 0.526 Chirality : 0.081 2.589 1632 Planarity : 0.007 0.182 1828 Dihedral : 5.182 55.750 1425 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.82 % Favored : 94.85 % Rotamer: Outliers : 4.44 % Allowed : 33.15 % Favored : 62.41 % Cbeta Deviations : 0.17 % 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: -0.01 (0.24), residues: 1268 helix: 0.78 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.28 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 314 TYR 0.014 0.001 TYR C 22 PHE 0.321 0.003 PHE D 315 TRP 0.027 0.002 TRP B 255 HIS 0.006 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00679 (10768) covalent geometry : angle 1.13313 (14656) hydrogen bonds : bond 0.04417 ( 512) hydrogen bonds : angle 4.11385 ( 1457) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8330 (OUTLIER) cc_final: 0.8105 (p) REVERT: B 345 PHE cc_start: 0.8851 (m-80) cc_final: 0.8588 (m-80) REVERT: B 349 ILE cc_start: 0.9119 (mp) cc_final: 0.8878 (mp) REVERT: C 111 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8379 (tm-30) REVERT: C 201 LEU cc_start: 0.8312 (mm) cc_final: 0.8003 (mm) REVERT: C 210 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: D 53 ASP cc_start: 0.6615 (t0) cc_final: 0.6351 (t0) REVERT: D 430 MET cc_start: 0.8834 (mmm) cc_final: 0.7812 (mtm) outliers start: 33 outliers final: 25 residues processed: 209 average time/residue: 0.4075 time to fit residues: 94.1718 Evaluate side-chains 208 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 447 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 0.9980 chunk 56 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 115 optimal weight: 0.3980 chunk 123 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 0.0370 chunk 68 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS C 327 HIS D 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.131181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099534 restraints weight = 89495.573| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 4.14 r_work: 0.3170 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.381 10768 Z= 0.291 Angle : 1.133 69.287 14656 Z= 0.526 Chirality : 0.081 2.589 1632 Planarity : 0.007 0.182 1828 Dihedral : 5.182 55.750 1425 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.82 % Favored : 94.85 % Rotamer: Outliers : 3.99 % Allowed : 33.61 % Favored : 62.41 % Cbeta Deviations : 0.17 % 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: -0.01 (0.24), residues: 1268 helix: 0.78 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.28 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 314 TYR 0.014 0.001 TYR C 22 PHE 0.321 0.003 PHE D 315 TRP 0.027 0.002 TRP B 255 HIS 0.006 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00679 (10768) covalent geometry : angle 1.13313 (14656) hydrogen bonds : bond 0.04417 ( 512) hydrogen bonds : angle 4.11385 ( 1457) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4478.89 seconds wall clock time: 76 minutes 53.20 seconds (4613.20 seconds total)