Starting phenix.real_space_refine on Mon Jul 28 13:45:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pqt_13604/07_2025/7pqt_13604.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pqt_13604/07_2025/7pqt_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7pqt_13604/07_2025/7pqt_13604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pqt_13604/07_2025/7pqt_13604.map" model { file = "/net/cci-nas-00/data/ceres_data/7pqt_13604/07_2025/7pqt_13604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pqt_13604/07_2025/7pqt_13604.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 11.25, per 1000 atoms: 1.08 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: 2.35 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 1.04 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: 3.40 Time building geometry restraints manager: 2.84 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: 3.040 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 32.720 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.880 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.008 0.002 TRP A 393 HIS 0.006 0.001 HIS B 66 PHE 0.025 0.002 PHE C 56 TYR 0.022 0.002 TYR C 22 ARG 0.010 0.001 ARG C 320 Details of bonding type rmsd hydrogen bonds : bond 0.17200 ( 512) hydrogen bonds : angle 5.93393 ( 1457) covalent geometry : bond 0.01073 (10768) covalent geometry : angle 0.86647 (14656) *********************** 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 : 1.062 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: 0.6659 (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: 0.9106 time to fit residues: 278.9595 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 : 1.127 ------------------------------------------------------------------------------- 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 104 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 37 optimal weight: 0.2980 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 112 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.129277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.097832 restraints weight = 74991.934| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.91 r_work: 0.3152 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 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 = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10768 Z= 0.147 Angle : 0.722 14.186 14656 Z= 0.362 Chirality : 0.044 0.177 1632 Planarity : 0.006 0.049 1828 Dihedral : 8.150 57.781 1503 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.07 % Favored : 94.61 % Rotamer: Outliers : 6.43 % Allowed : 30.16 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.85 (0.21), residues: 1268 helix: -0.72 (0.17), residues: 800 sheet: None (None), residues: 0 loop : -1.98 (0.24), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 106 HIS 0.003 0.001 HIS A 112 PHE 0.023 0.002 PHE A 315 TYR 0.019 0.002 TYR C 22 ARG 0.008 0.001 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.04852 ( 512) hydrogen bonds : angle 4.32184 ( 1457) covalent geometry : bond 0.00338 (10768) covalent geometry : angle 0.72218 (14656) *********************** 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 258 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 203 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: A 54 GLU cc_start: 0.8201 (pt0) cc_final: 0.7969 (pt0) REVERT: A 450 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8200 (mt0) REVERT: B 10 ILE cc_start: 0.8385 (pp) cc_final: 0.8183 (pt) REVERT: B 49 ASP cc_start: 0.7412 (m-30) cc_final: 0.7199 (m-30) REVERT: B 345 PHE cc_start: 0.8918 (m-80) cc_final: 0.8632 (m-80) REVERT: B 349 ILE cc_start: 0.9107 (mt) cc_final: 0.8903 (mp) REVERT: C 54 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7606 (pt0) REVERT: C 210 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7696 (mp0) REVERT: C 380 GLU cc_start: 0.6710 (OUTLIER) cc_final: 0.6108 (mp0) REVERT: D 53 ASP cc_start: 0.6510 (t0) cc_final: 0.6271 (t0) outliers start: 55 outliers final: 24 residues processed: 237 average time/residue: 1.1833 time to fit residues: 308.4019 Evaluate side-chains 213 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 412 SER 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 346 LEU 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 209 LEU 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 338 LEU 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 8 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 115 optimal weight: 0.4980 chunk 95 optimal weight: 0.1980 chunk 2 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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 = 0.129993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.098591 restraints weight = 85767.540| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 4.45 r_work: 0.3147 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1836 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= 0.143 Angle : 0.713 14.914 14656 Z= 0.349 Chirality : 0.044 0.178 1632 Planarity : 0.005 0.042 1828 Dihedral : 6.718 58.164 1442 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.49 % Favored : 95.18 % Rotamer: Outliers : 6.70 % Allowed : 29.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.22), residues: 1268 helix: -0.08 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -1.68 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 255 HIS 0.004 0.001 HIS A 112 PHE 0.023 0.002 PHE A 260 TYR 0.023 0.001 TYR C 48 ARG 0.007 0.001 ARG A 263 Details of bonding type rmsd hydrogen bonds : bond 0.04537 ( 512) hydrogen bonds : angle 4.20754 ( 1457) covalent geometry : bond 0.00335 (10768) covalent geometry : angle 0.71255 (14656) *********************** 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 266 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 208 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8283 (OUTLIER) cc_final: 0.8050 (p) REVERT: A 54 GLU cc_start: 0.8154 (pt0) cc_final: 0.7918 (pt0) REVERT: A 450 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8122 (mt0) REVERT: B 24 SER cc_start: 0.8532 (OUTLIER) cc_final: 0.8293 (p) REVERT: B 49 ASP cc_start: 0.7459 (m-30) cc_final: 0.7150 (m-30) REVERT: B 345 PHE cc_start: 0.8947 (m-80) cc_final: 0.8672 (m-80) REVERT: C 54 GLU cc_start: 0.7754 (pt0) cc_final: 0.7524 (pt0) REVERT: C 210 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: D 53 ASP cc_start: 0.6529 (t0) cc_final: 0.6305 (t0) outliers start: 58 outliers final: 27 residues processed: 242 average time/residue: 0.8670 time to fit residues: 231.6472 Evaluate side-chains 228 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 197 time to evaluate : 1.172 ------------------------------------------------------------------------------- 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 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 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 C residue 21 THR 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 254 VAL 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 C residue 451 LYS 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 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 63 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 42 optimal weight: 0.0370 chunk 99 optimal weight: 0.0870 chunk 76 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 37 optimal weight: 0.2980 chunk 23 optimal weight: 0.6980 chunk 110 optimal weight: 0.0970 overall best weight: 0.2234 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 ASN C 112 HIS C 327 HIS 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 = 0.3804 r_free = 0.3804 target = 0.132946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.101184 restraints weight = 97111.685| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 4.60 r_work: 0.3184 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2370 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= 0.124 Angle : 0.707 13.396 14656 Z= 0.341 Chirality : 0.042 0.199 1632 Planarity : 0.005 0.037 1828 Dihedral : 6.133 54.295 1438 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.25 % Favored : 95.42 % Rotamer: Outliers : 5.25 % Allowed : 31.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.23), residues: 1268 helix: 0.31 (0.19), residues: 784 sheet: None (None), residues: 0 loop : -1.42 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 255 HIS 0.004 0.001 HIS D 112 PHE 0.020 0.001 PHE C 315 TYR 0.027 0.001 TYR C 48 ARG 0.006 0.001 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 512) hydrogen bonds : angle 4.12561 ( 1457) covalent geometry : bond 0.00278 (10768) covalent geometry : angle 0.70704 (14656) *********************** 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 255 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 213 time to evaluate : 1.165 Fit side-chains REVERT: A 54 GLU cc_start: 0.8017 (pt0) cc_final: 0.7785 (pt0) REVERT: A 341 SER cc_start: 0.8655 (m) cc_final: 0.8367 (p) REVERT: B 49 ASP cc_start: 0.7455 (m-30) cc_final: 0.7183 (m-30) REVERT: B 54 GLU cc_start: 0.7722 (pt0) cc_final: 0.7452 (pt0) REVERT: B 210 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7408 (mp0) REVERT: B 345 PHE cc_start: 0.8814 (m-80) cc_final: 0.8592 (m-80) REVERT: C 54 GLU cc_start: 0.7732 (pt0) cc_final: 0.6937 (pm20) REVERT: C 210 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: C 314 ARG cc_start: 0.7063 (ptp-110) cc_final: 0.6780 (ptp-110) REVERT: D 53 ASP cc_start: 0.6500 (t0) cc_final: 0.6273 (t0) REVERT: D 430 MET cc_start: 0.8685 (mmm) cc_final: 0.7743 (mtm) outliers start: 42 outliers final: 15 residues processed: 236 average time/residue: 0.8626 time to fit residues: 225.0308 Evaluate side-chains 213 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 197 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 427 THR 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 346 LEU Chi-restraints excluded: chain C residue 389 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 17 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 92 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN C 13 ASN C 327 HIS 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 = 0.3742 r_free = 0.3742 target = 0.128264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.096159 restraints weight = 84406.035| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 4.11 r_work: 0.3122 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10768 Z= 0.200 Angle : 0.727 12.296 14656 Z= 0.365 Chirality : 0.046 0.223 1632 Planarity : 0.005 0.043 1828 Dihedral : 5.645 56.033 1431 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.82 % Favored : 94.85 % Rotamer: Outliers : 6.34 % Allowed : 30.25 % Favored : 63.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.23), residues: 1268 helix: 0.33 (0.19), residues: 760 sheet: -0.17 (0.72), residues: 40 loop : -1.31 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 255 HIS 0.009 0.001 HIS C 112 PHE 0.024 0.002 PHE B 55 TYR 0.021 0.002 TYR C 22 ARG 0.005 0.001 ARG A 320 Details of bonding type rmsd hydrogen bonds : bond 0.05074 ( 512) hydrogen bonds : angle 4.25404 ( 1457) covalent geometry : bond 0.00474 (10768) covalent geometry : angle 0.72726 (14656) *********************** 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 251 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 24 SER cc_start: 0.8395 (OUTLIER) cc_final: 0.8075 (p) REVERT: A 54 GLU cc_start: 0.8197 (pt0) cc_final: 0.7981 (pt0) REVERT: A 107 MET cc_start: 0.8473 (mmm) cc_final: 0.8264 (mmm) REVERT: B 201 LEU cc_start: 0.8212 (mm) cc_final: 0.8003 (mm) REVERT: C 110 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.8116 (tpt170) REVERT: C 210 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7710 (mp0) REVERT: D 53 ASP cc_start: 0.6525 (t0) cc_final: 0.6263 (t0) REVERT: D 213 GLU cc_start: 0.7887 (tp30) cc_final: 0.7485 (mm-30) outliers start: 54 outliers final: 28 residues processed: 235 average time/residue: 0.8887 time to fit residues: 229.6825 Evaluate side-chains 217 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 186 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 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 21 THR Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 350 ILE 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 110 ARG 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 257 THR 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 D residue 11 VAL Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 328 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 95 optimal weight: 0.0870 chunk 106 optimal weight: 2.9990 chunk 123 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 C 327 HIS 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 = 0.3770 r_free = 0.3770 target = 0.130285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.098442 restraints weight = 79324.380| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 4.02 r_work: 0.3160 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3161 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10768 Z= 0.145 Angle : 0.695 13.137 14656 Z= 0.343 Chirality : 0.044 0.186 1632 Planarity : 0.005 0.046 1828 Dihedral : 5.216 51.161 1428 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.58 % Favored : 95.10 % Rotamer: Outliers : 4.62 % Allowed : 32.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.23), residues: 1268 helix: 0.52 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -1.37 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 255 HIS 0.007 0.001 HIS C 112 PHE 0.022 0.002 PHE A 260 TYR 0.014 0.001 TYR C 22 ARG 0.005 0.001 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.04368 ( 512) hydrogen bonds : angle 4.15264 ( 1457) covalent geometry : bond 0.00341 (10768) covalent geometry : angle 0.69459 (14656) *********************** 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 234 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 199 time to evaluate : 1.115 Fit side-chains revert: symmetry clash REVERT: A 24 SER cc_start: 0.8245 (OUTLIER) cc_final: 0.8003 (p) REVERT: A 54 GLU cc_start: 0.8092 (pt0) cc_final: 0.7853 (pt0) REVERT: A 107 MET cc_start: 0.8455 (mmm) cc_final: 0.8224 (mmm) REVERT: B 89 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.7976 (tt0) REVERT: C 54 GLU cc_start: 0.7707 (pt0) cc_final: 0.7388 (pt0) REVERT: C 210 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: D 53 ASP cc_start: 0.6474 (t0) cc_final: 0.6226 (t0) REVERT: D 430 MET cc_start: 0.8771 (mmm) cc_final: 0.7664 (mtm) outliers start: 35 outliers final: 23 residues processed: 222 average time/residue: 0.9070 time to fit residues: 221.7088 Evaluate side-chains 217 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 191 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 253 VAL 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 89 GLU Chi-restraints excluded: chain B residue 350 ILE 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 254 VAL Chi-restraints excluded: chain C residue 257 THR 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 D residue 258 PHE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 328 PHE Chi-restraints excluded: chain D residue 341 SER 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 1.9990 chunk 3 optimal weight: 0.0000 chunk 112 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 47 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 118 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 45 optimal weight: 0.0070 overall best weight: 0.4002 ------------------------------------------------------------------------------- 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 D 216 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.132295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.100705 restraints weight = 92232.066| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 4.49 r_work: 0.3180 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 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 = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10768 Z= 0.130 Angle : 0.697 12.679 14656 Z= 0.338 Chirality : 0.043 0.184 1632 Planarity : 0.005 0.039 1828 Dihedral : 5.016 51.030 1426 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.41 % Favored : 95.26 % Rotamer: Outliers : 4.17 % Allowed : 32.34 % Favored : 63.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.23), residues: 1268 helix: 0.66 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -1.25 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 255 HIS 0.006 0.001 HIS C 112 PHE 0.017 0.001 PHE A 260 TYR 0.013 0.001 TYR C 22 ARG 0.006 0.001 ARG A 326 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 512) hydrogen bonds : angle 4.09016 ( 1457) covalent geometry : bond 0.00301 (10768) covalent geometry : angle 0.69653 (14656) *********************** 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 233 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 210 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: D 53 ASP cc_start: 0.6639 (t0) cc_final: 0.6388 (t0) REVERT: D 213 GLU cc_start: 0.7942 (tp30) cc_final: 0.7506 (mm-30) REVERT: D 430 MET cc_start: 0.8812 (mmm) cc_final: 0.7784 (mtm) outliers start: 30 outliers final: 19 residues processed: 220 average time/residue: 0.8849 time to fit residues: 215.2027 Evaluate side-chains 217 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 VAL 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 321 ILE Chi-restraints excluded: chain B residue 350 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 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 328 PHE Chi-restraints excluded: chain D residue 341 SER Chi-restraints excluded: chain D residue 389 ILE 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 6 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 13 optimal weight: 0.0370 overall best weight: 1.1662 ------------------------------------------------------------------------------- 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 = 0.128930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.096950 restraints weight = 97150.063| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 4.50 r_work: 0.3118 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 10768 Z= 0.208 Angle : 0.743 13.472 14656 Z= 0.369 Chirality : 0.047 0.426 1632 Planarity : 0.005 0.047 1828 Dihedral : 5.031 49.858 1423 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.58 % Favored : 95.10 % Rotamer: Outliers : 4.89 % Allowed : 32.70 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.23), residues: 1268 helix: 0.66 (0.19), residues: 788 sheet: -0.12 (0.69), residues: 40 loop : -1.37 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 255 HIS 0.008 0.001 HIS C 112 PHE 0.048 0.002 PHE C 55 TYR 0.018 0.002 TYR C 22 ARG 0.012 0.001 ARG C 314 Details of bonding type rmsd hydrogen bonds : bond 0.05044 ( 512) hydrogen bonds : angle 4.23968 ( 1457) covalent geometry : bond 0.00494 (10768) covalent geometry : angle 0.74262 (14656) *********************** 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 235 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 89 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: C 54 GLU cc_start: 0.7841 (pt0) cc_final: 0.7543 (pt0) REVERT: C 210 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: D 53 ASP cc_start: 0.6664 (t0) cc_final: 0.6374 (t0) REVERT: D 430 MET cc_start: 0.8929 (mmm) cc_final: 0.7924 (mtm) outliers start: 38 outliers final: 22 residues processed: 227 average time/residue: 0.8373 time to fit residues: 210.2521 Evaluate side-chains 211 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 89 GLU Chi-restraints excluded: chain B residue 108 THR 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 254 VAL Chi-restraints excluded: chain C residue 257 THR 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 341 SER 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 447 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 103 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 99 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS B 438 ASN C 327 HIS 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 = 0.3769 r_free = 0.3769 target = 0.129917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.098065 restraints weight = 86574.328| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 4.09 r_work: 0.3146 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 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 = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10768 Z= 0.175 Angle : 0.734 13.814 14656 Z= 0.361 Chirality : 0.046 0.465 1632 Planarity : 0.005 0.045 1828 Dihedral : 4.851 35.177 1421 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.25 % Favored : 95.42 % Rotamer: Outliers : 4.53 % Allowed : 32.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.23), residues: 1268 helix: 0.70 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.34 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 255 HIS 0.007 0.001 HIS C 112 PHE 0.017 0.002 PHE C 55 TYR 0.017 0.001 TYR C 22 ARG 0.008 0.001 ARG C 314 Details of bonding type rmsd hydrogen bonds : bond 0.04732 ( 512) hydrogen bonds : angle 4.21372 ( 1457) covalent geometry : bond 0.00416 (10768) covalent geometry : angle 0.73360 (14656) *********************** 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 221 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 GLU cc_start: 0.8044 (pt0) cc_final: 0.7763 (pm20) REVERT: A 89 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.8006 (tt0) REVERT: B 89 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.8043 (tt0) REVERT: C 54 GLU cc_start: 0.7780 (pt0) cc_final: 0.7491 (pt0) REVERT: C 210 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: D 53 ASP cc_start: 0.6663 (t0) cc_final: 0.6368 (t0) REVERT: D 430 MET cc_start: 0.8902 (mmm) cc_final: 0.7840 (mtm) outliers start: 34 outliers final: 23 residues processed: 212 average time/residue: 0.8634 time to fit residues: 201.9235 Evaluate side-chains 207 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU 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 89 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 350 ILE 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 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 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 341 SER 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 447 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 32 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 104 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS B 438 ASN C 327 HIS 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 = 0.3761 r_free = 0.3761 target = 0.129345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.097396 restraints weight = 88092.680| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 4.11 r_work: 0.3137 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10768 Z= 0.195 Angle : 0.752 15.084 14656 Z= 0.369 Chirality : 0.046 0.397 1632 Planarity : 0.005 0.046 1828 Dihedral : 4.910 36.592 1421 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.41 % Favored : 95.26 % Rotamer: Outliers : 3.99 % Allowed : 33.61 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.23), residues: 1268 helix: 0.70 (0.19), residues: 788 sheet: -0.23 (0.68), residues: 40 loop : -1.37 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 255 HIS 0.007 0.001 HIS C 112 PHE 0.021 0.002 PHE B 55 TYR 0.018 0.002 TYR C 22 ARG 0.009 0.001 ARG C 314 Details of bonding type rmsd hydrogen bonds : bond 0.04936 ( 512) hydrogen bonds : angle 4.24909 ( 1457) covalent geometry : bond 0.00464 (10768) covalent geometry : angle 0.75221 (14656) ********************** 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 214 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 186 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8011 (tt0) REVERT: B 89 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8054 (tt0) REVERT: C 54 GLU cc_start: 0.7806 (pt0) cc_final: 0.7517 (pt0) REVERT: C 210 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7762 (mp0) REVERT: D 53 ASP cc_start: 0.6676 (t0) cc_final: 0.6382 (t0) REVERT: D 430 MET cc_start: 0.8932 (mmm) cc_final: 0.7879 (mtm) outliers start: 28 outliers final: 23 residues processed: 207 average time/residue: 1.4226 time to fit residues: 328.6858 Evaluate side-chains 207 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 181 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 GLU 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 89 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 350 ILE 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 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 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 447 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 29 optimal weight: 0.8980 chunk 114 optimal weight: 0.9990 chunk 118 optimal weight: 0.0970 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 50 optimal weight: 0.2980 chunk 79 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 HIS B 438 ASN C 327 HIS 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 = 0.3790 r_free = 0.3790 target = 0.131520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.099629 restraints weight = 98029.012| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 4.55 r_work: 0.3159 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 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 = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10768 Z= 0.145 Angle : 0.719 13.792 14656 Z= 0.350 Chirality : 0.044 0.277 1632 Planarity : 0.005 0.045 1828 Dihedral : 4.783 33.145 1421 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.33 % Favored : 95.34 % Rotamer: Outliers : 3.35 % Allowed : 34.06 % Favored : 62.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.24), residues: 1268 helix: 0.78 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -1.22 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 255 HIS 0.006 0.001 HIS C 112 PHE 0.017 0.002 PHE C 55 TYR 0.015 0.001 TYR C 22 ARG 0.009 0.001 ARG C 314 Details of bonding type rmsd hydrogen bonds : bond 0.04311 ( 512) hydrogen bonds : angle 4.16258 ( 1457) covalent geometry : bond 0.00341 (10768) covalent geometry : angle 0.71891 (14656) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9724.04 seconds wall clock time: 170 minutes 50.32 seconds (10250.32 seconds total)