Starting phenix.real_space_refine on Fri Feb 14 16:20:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pqt_13604/02_2025/7pqt_13604.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pqt_13604/02_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_13604/02_2025/7pqt_13604.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pqt_13604/02_2025/7pqt_13604.map" model { file = "/net/cci-nas-00/data/ceres_data/7pqt_13604/02_2025/7pqt_13604.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pqt_13604/02_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-5592/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: 11.45, per 1000 atoms: 1.09 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: 2.53 Conformation dependent library (CDL) restraints added in 2.5 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: 0.96 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: 3.27 Time building geometry restraints manager: 2.98 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 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: 0.480 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 32.400 Find NCS groups from input model: 0.520 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: 0.000 Load rotamer database and sin/cos tables:11.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.620 ------------------------------------------------------------------------------- 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= 0.696 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 *********************** 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 : 1.040 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: 0.9357 time to fit residues: 286.9480 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 : 1.113 ------------------------------------------------------------------------------- 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 = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.097822 restraints weight = 74992.151| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 3.91 r_work: 0.3151 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 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 = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- 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= 0.215 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 *********************** 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 : 1.086 Fit side-chains revert: symmetry clash REVERT: A 54 GLU cc_start: 0.8202 (pt0) cc_final: 0.7970 (pt0) REVERT: A 450 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8204 (mt0) REVERT: B 10 ILE cc_start: 0.8389 (pp) cc_final: 0.8186 (pt) REVERT: B 49 ASP cc_start: 0.7409 (m-30) cc_final: 0.7194 (m-30) REVERT: B 345 PHE cc_start: 0.8919 (m-80) cc_final: 0.8632 (m-80) REVERT: B 349 ILE cc_start: 0.9106 (mt) cc_final: 0.8901 (mp) REVERT: C 54 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7610 (pt0) REVERT: C 210 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7698 (mp0) REVERT: C 380 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.6126 (mp0) REVERT: D 53 ASP cc_start: 0.6505 (t0) cc_final: 0.6266 (t0) outliers start: 55 outliers final: 24 residues processed: 237 average time/residue: 0.9457 time to fit residues: 245.8325 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 : 1.203 ------------------------------------------------------------------------------- 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: 5.9990 chunk 25 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 115 optimal weight: 0.5980 chunk 95 optimal weight: 0.0870 chunk 2 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.129952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.098235 restraints weight = 85791.358| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 4.35 r_work: 0.3147 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1826 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= 0.213 Angle : 0.713 15.169 14656 Z= 0.349 Chirality : 0.044 0.159 1632 Planarity : 0.005 0.043 1828 Dihedral : 6.732 58.709 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 : 6.52 % Allowed : 29.98 % 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: -1.10 (0.22), residues: 1268 helix: -0.10 (0.19), residues: 780 sheet: None (None), residues: 0 loop : -1.69 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 255 HIS 0.003 0.001 HIS A 112 PHE 0.022 0.002 PHE A 260 TYR 0.021 0.001 TYR C 48 ARG 0.007 0.001 ARG A 263 *********************** 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 263 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 207 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8271 (OUTLIER) cc_final: 0.8024 (p) REVERT: A 54 GLU cc_start: 0.8152 (pt0) cc_final: 0.7931 (pt0) REVERT: A 450 GLN cc_start: 0.8445 (OUTLIER) cc_final: 0.8136 (mt0) REVERT: B 24 SER cc_start: 0.8510 (OUTLIER) cc_final: 0.8257 (p) REVERT: B 49 ASP cc_start: 0.7422 (m-30) cc_final: 0.7101 (m-30) REVERT: B 345 PHE cc_start: 0.8918 (m-80) cc_final: 0.8640 (m-80) REVERT: C 54 GLU cc_start: 0.7741 (pt0) cc_final: 0.7461 (pt0) REVERT: C 210 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: C 314 ARG cc_start: 0.6955 (OUTLIER) cc_final: 0.6739 (ptp-110) REVERT: D 53 ASP cc_start: 0.6489 (t0) cc_final: 0.6268 (t0) outliers start: 56 outliers final: 27 residues processed: 239 average time/residue: 0.9224 time to fit residues: 242.1463 Evaluate side-chains 228 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 196 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 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 314 ARG Chi-restraints excluded: chain C residue 321 ILE Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 257 THR Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 328 PHE Chi-restraints excluded: chain D residue 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: 1.9990 chunk 99 optimal weight: 0.2980 chunk 76 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 110 optimal weight: 0.0370 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 ASN C 327 HIS D 45 HIS D 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.129746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.097652 restraints weight = 97741.039| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 4.39 r_work: 0.3133 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10768 Z= 0.237 Angle : 0.725 13.383 14656 Z= 0.355 Chirality : 0.044 0.178 1632 Planarity : 0.005 0.045 1828 Dihedral : 6.374 55.647 1438 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.66 % Favored : 95.02 % Rotamer: Outliers : 6.52 % Allowed : 30.53 % Favored : 62.95 % 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: -0.67 (0.23), residues: 1268 helix: 0.20 (0.19), residues: 760 sheet: -0.16 (0.72), residues: 40 loop : -1.44 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 255 HIS 0.004 0.001 HIS A 112 PHE 0.019 0.002 PHE C 315 TYR 0.017 0.001 TYR C 22 ARG 0.006 0.001 ARG A 326 *********************** 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 261 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 205 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 SER cc_start: 0.8306 (OUTLIER) cc_final: 0.8026 (p) REVERT: A 54 GLU cc_start: 0.8169 (pt0) cc_final: 0.7945 (pt0) REVERT: A 450 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.8195 (mt0) REVERT: B 24 SER cc_start: 0.8529 (OUTLIER) cc_final: 0.8265 (p) REVERT: B 49 ASP cc_start: 0.7402 (m-30) cc_final: 0.7105 (m-30) REVERT: B 345 PHE cc_start: 0.8842 (m-80) cc_final: 0.8578 (m-80) REVERT: B 349 ILE cc_start: 0.9040 (mp) cc_final: 0.8816 (mp) REVERT: C 54 GLU cc_start: 0.7759 (pt0) cc_final: 0.7504 (pt0) REVERT: C 88 GLU cc_start: 0.8619 (tm-30) cc_final: 0.8393 (tt0) REVERT: C 110 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8030 (tpt170) REVERT: C 210 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: C 314 ARG cc_start: 0.6941 (OUTLIER) cc_final: 0.6723 (ptp-110) REVERT: D 53 ASP cc_start: 0.6494 (t0) cc_final: 0.6258 (t0) REVERT: D 430 MET cc_start: 0.8826 (mmm) cc_final: 0.7882 (mtm) outliers start: 56 outliers final: 31 residues processed: 240 average time/residue: 0.9222 time to fit residues: 243.7067 Evaluate side-chains 230 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 193 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 SER Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain C residue 21 THR 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 254 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 427 THR 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 389 ILE Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 17 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 96 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 107 optimal weight: 0.3980 chunk 60 optimal weight: 0.0030 chunk 7 optimal weight: 2.9990 chunk 104 optimal weight: 4.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN C 327 HIS D 45 HIS D 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.130810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.098815 restraints weight = 84545.569| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 4.15 r_work: 0.3161 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 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 = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2171 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= 0.205 Angle : 0.695 12.973 14656 Z= 0.341 Chirality : 0.043 0.175 1632 Planarity : 0.005 0.041 1828 Dihedral : 6.108 55.511 1438 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.66 % Favored : 95.02 % Rotamer: Outliers : 5.98 % Allowed : 30.80 % Favored : 63.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.48 (0.23), residues: 1268 helix: 0.35 (0.19), residues: 784 sheet: None (None), residues: 0 loop : -1.35 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 255 HIS 0.004 0.001 HIS A 112 PHE 0.017 0.001 PHE D 315 TYR 0.030 0.001 TYR C 48 ARG 0.005 0.001 ARG A 326 *********************** 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 250 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 200 time to evaluate : 1.161 Fit side-chains revert: symmetry clash REVERT: A 24 SER cc_start: 0.8277 (OUTLIER) cc_final: 0.8001 (p) REVERT: A 54 GLU cc_start: 0.8094 (pt0) cc_final: 0.7864 (pt0) REVERT: A 107 MET cc_start: 0.8451 (mmm) cc_final: 0.8234 (mmm) REVERT: A 341 SER cc_start: 0.8684 (m) cc_final: 0.8408 (p) REVERT: B 24 SER cc_start: 0.8507 (OUTLIER) cc_final: 0.8248 (p) REVERT: B 49 ASP cc_start: 0.7408 (m-30) cc_final: 0.7137 (m-30) REVERT: B 345 PHE cc_start: 0.8828 (m-80) cc_final: 0.8547 (m-80) REVERT: B 349 ILE cc_start: 0.9013 (mp) cc_final: 0.8755 (mp) REVERT: C 54 GLU cc_start: 0.7744 (pt0) cc_final: 0.7424 (pt0) REVERT: C 210 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: C 314 ARG cc_start: 0.6966 (OUTLIER) cc_final: 0.6765 (ptp-110) REVERT: D 53 ASP cc_start: 0.6466 (t0) cc_final: 0.6234 (t0) REVERT: D 213 GLU cc_start: 0.7912 (tp30) cc_final: 0.7536 (mm-30) outliers start: 50 outliers final: 27 residues processed: 232 average time/residue: 0.9282 time to fit residues: 237.5133 Evaluate side-chains 216 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 185 time to evaluate : 1.151 ------------------------------------------------------------------------------- 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 B residue 21 THR 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 257 THR Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 427 THR 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 318 ILE Chi-restraints excluded: chain D residue 328 PHE Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 427 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 85 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 111 GLN C 327 HIS D 45 HIS D 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.129019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.097161 restraints weight = 79525.805| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 4.00 r_work: 0.3139 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3139 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3139 r_free = 0.3139 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3139 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10768 Z= 0.264 Angle : 0.710 13.359 14656 Z= 0.353 Chirality : 0.045 0.182 1632 Planarity : 0.005 0.047 1828 Dihedral : 5.848 56.443 1434 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.58 % Favored : 95.10 % Rotamer: Outliers : 6.16 % Allowed : 30.89 % Favored : 62.95 % 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: -0.31 (0.23), residues: 1268 helix: 0.46 (0.20), residues: 760 sheet: -0.15 (0.72), residues: 40 loop : -1.22 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 255 HIS 0.004 0.001 HIS A 112 PHE 0.017 0.002 PHE B 55 TYR 0.018 0.001 TYR C 22 ARG 0.005 0.001 ARG C 326 *********************** 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 245 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 193 time to evaluate : 1.091 Fit side-chains revert: symmetry clash REVERT: A 24 SER cc_start: 0.8344 (OUTLIER) cc_final: 0.8029 (p) REVERT: A 54 GLU cc_start: 0.8150 (pt0) cc_final: 0.7914 (pt0) REVERT: A 107 MET cc_start: 0.8470 (mmm) cc_final: 0.8256 (mmm) REVERT: B 24 SER cc_start: 0.8545 (OUTLIER) cc_final: 0.8268 (p) REVERT: B 89 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8023 (tt0) REVERT: B 210 GLU cc_start: 0.8095 (mp0) cc_final: 0.7323 (mp0) REVERT: B 349 ILE cc_start: 0.9024 (mp) cc_final: 0.8776 (mp) REVERT: C 110 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.8089 (tpt170) REVERT: C 210 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7654 (mp0) REVERT: C 314 ARG cc_start: 0.6981 (OUTLIER) cc_final: 0.6764 (ptp-110) REVERT: D 53 ASP cc_start: 0.6472 (t0) cc_final: 0.6211 (t0) REVERT: D 430 MET cc_start: 0.8876 (mmm) cc_final: 0.7824 (mtm) outliers start: 52 outliers final: 32 residues processed: 227 average time/residue: 0.9081 time to fit residues: 226.8331 Evaluate side-chains 223 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 1.046 ------------------------------------------------------------------------------- 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 B residue 24 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 346 LEU 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 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 254 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 314 ARG Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 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: 0.6980 chunk 112 optimal weight: 0.9980 chunk 73 optimal weight: 0.0060 chunk 47 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- 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 D 216 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.131010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.099443 restraints weight = 92088.240| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 4.46 r_work: 0.3163 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 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 : 0.003 0.041 10768 Z= 0.208 Angle : 0.699 13.620 14656 Z= 0.343 Chirality : 0.043 0.175 1632 Planarity : 0.005 0.044 1828 Dihedral : 5.536 50.974 1431 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.33 % Favored : 95.34 % Rotamer: Outliers : 5.62 % Allowed : 31.07 % Favored : 63.32 % 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: -0.21 (0.23), residues: 1268 helix: 0.59 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.31 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 255 HIS 0.004 0.001 HIS A 112 PHE 0.015 0.002 PHE A 315 TYR 0.015 0.001 TYR C 22 ARG 0.006 0.001 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2536 Ramachandran restraints generated. 1268 Oldfield, 0 Emsley, 1268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 196 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: B 24 SER cc_start: 0.8571 (OUTLIER) cc_final: 0.8359 (p) REVERT: B 89 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.8039 (tt0) REVERT: B 345 PHE cc_start: 0.8917 (m-80) cc_final: 0.8659 (m-80) REVERT: B 349 ILE cc_start: 0.9134 (mp) cc_final: 0.8901 (mp) REVERT: C 210 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7759 (mp0) REVERT: D 53 ASP cc_start: 0.6622 (t0) cc_final: 0.6357 (t0) REVERT: D 213 GLU cc_start: 0.7948 (tp30) cc_final: 0.7560 (mm-30) REVERT: D 430 MET cc_start: 0.8895 (mmm) cc_final: 0.7866 (mtm) outliers start: 46 outliers final: 32 residues processed: 226 average time/residue: 0.9269 time to fit residues: 230.7889 Evaluate side-chains 218 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 389 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 0.2980 chunk 69 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.129593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.097732 restraints weight = 97183.293| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 4.57 r_work: 0.3131 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 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 = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10768 Z= 0.273 Angle : 0.731 13.670 14656 Z= 0.360 Chirality : 0.045 0.187 1632 Planarity : 0.005 0.048 1828 Dihedral : 5.554 50.676 1430 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.74 % Favored : 94.93 % Rotamer: Outliers : 5.53 % Allowed : 31.43 % 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: -0.12 (0.23), residues: 1268 helix: 0.69 (0.19), residues: 788 sheet: -0.18 (0.70), residues: 40 loop : -1.41 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 255 HIS 0.004 0.001 HIS A 112 PHE 0.015 0.002 PHE B 55 TYR 0.017 0.001 TYR C 22 ARG 0.005 0.001 ARG C 110 *********************** 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 229 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 184 time to evaluate : 1.149 Fit side-chains revert: symmetry clash REVERT: A 54 GLU cc_start: 0.8117 (pt0) cc_final: 0.7810 (pm20) REVERT: B 24 SER cc_start: 0.8620 (OUTLIER) cc_final: 0.8386 (p) REVERT: B 89 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8052 (tt0) REVERT: B 345 PHE cc_start: 0.8902 (m-80) cc_final: 0.8665 (m-80) REVERT: B 349 ILE cc_start: 0.9146 (mp) cc_final: 0.8921 (mp) REVERT: C 210 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7769 (mp0) REVERT: D 53 ASP cc_start: 0.6664 (t0) cc_final: 0.6383 (t0) REVERT: D 430 MET cc_start: 0.8955 (mmm) cc_final: 0.7951 (mtm) outliers start: 45 outliers final: 29 residues processed: 216 average time/residue: 0.8758 time to fit residues: 208.5984 Evaluate side-chains 215 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 1.067 ------------------------------------------------------------------------------- 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 389 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain B residue 21 THR Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain 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 257 THR Chi-restraints excluded: chain C residue 349 ILE Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 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 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: 1.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 103 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 50 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 123 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 HIS C 327 HIS D 45 HIS D 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.131244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099619 restraints weight = 86525.922| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 4.31 r_work: 0.3168 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2401 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= 0.215 Angle : 0.718 13.172 14656 Z= 0.349 Chirality : 0.043 0.251 1632 Planarity : 0.005 0.044 1828 Dihedral : 5.313 57.607 1427 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.25 % Favored : 95.42 % Rotamer: Outliers : 4.35 % Allowed : 32.25 % 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: -0.02 (0.24), residues: 1268 helix: 0.76 (0.19), residues: 792 sheet: None (None), residues: 0 loop : -1.29 (0.26), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 255 HIS 0.003 0.001 HIS A 112 PHE 0.018 0.002 PHE B 55 TYR 0.016 0.001 TYR C 22 ARG 0.008 0.001 ARG B 332 *********************** 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 233 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 201 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: B 24 SER cc_start: 0.8567 (OUTLIER) cc_final: 0.8359 (p) REVERT: B 89 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: B 345 PHE cc_start: 0.8868 (m-80) cc_final: 0.8612 (m-80) REVERT: B 349 ILE cc_start: 0.9135 (mp) cc_final: 0.8905 (mp) REVERT: C 54 GLU cc_start: 0.7792 (pt0) cc_final: 0.7512 (pt0) REVERT: C 210 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: D 53 ASP cc_start: 0.6653 (t0) cc_final: 0.6383 (t0) REVERT: D 430 MET cc_start: 0.8910 (mmm) cc_final: 0.7866 (mtm) outliers start: 32 outliers final: 24 residues processed: 224 average time/residue: 0.9129 time to fit residues: 225.3108 Evaluate side-chains 208 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 389 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 341 SER Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain 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 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 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: 1.9990 chunk 120 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 104 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 13 ASN C 327 HIS D 45 HIS D 111 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.128125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.096393 restraints weight = 88126.028| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 4.07 r_work: 0.3120 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10768 Z= 0.374 Angle : 0.780 13.217 14656 Z= 0.386 Chirality : 0.048 0.242 1632 Planarity : 0.005 0.048 1828 Dihedral : 5.570 54.298 1427 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.07 % Favored : 94.61 % Rotamer: Outliers : 4.35 % Allowed : 32.97 % Favored : 62.68 % 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: -0.18 (0.23), residues: 1268 helix: 0.60 (0.19), residues: 760 sheet: -0.30 (0.69), residues: 40 loop : -1.22 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 255 HIS 0.010 0.001 HIS C 112 PHE 0.022 0.002 PHE B 55 TYR 0.019 0.002 TYR C 22 ARG 0.011 0.001 ARG A 326 ********************** 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 213 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: B 24 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8318 (p) REVERT: B 89 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.8072 (tt0) REVERT: B 345 PHE cc_start: 0.8906 (m-80) cc_final: 0.8630 (m-80) REVERT: B 349 ILE cc_start: 0.9148 (mp) cc_final: 0.8891 (mp) REVERT: C 210 GLU cc_start: 0.8063 (OUTLIER) cc_final: 0.7782 (mp0) REVERT: D 430 MET cc_start: 0.8990 (mmm) cc_final: 0.7955 (mtm) outliers start: 32 outliers final: 22 residues processed: 206 average time/residue: 0.8796 time to fit residues: 200.5280 Evaluate side-chains 204 residues out of total 1072 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 1.129 ------------------------------------------------------------------------------- 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 389 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain B residue 24 SER Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 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 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 108 THR 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: 1.9990 chunk 114 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 = 0.3758 r_free = 0.3758 target = 0.129257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.097344 restraints weight = 97919.626| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 4.57 r_work: 0.3122 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 10768 Z= 0.289 Angle : 0.754 13.123 14656 Z= 0.371 Chirality : 0.046 0.246 1632 Planarity : 0.005 0.047 1828 Dihedral : 5.527 55.877 1427 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.58 % Favored : 95.10 % Rotamer: Outliers : 4.26 % Allowed : 32.88 % 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: -0.10 (0.23), residues: 1268 helix: 0.67 (0.19), residues: 784 sheet: -0.22 (0.69), residues: 40 loop : -1.31 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 255 HIS 0.008 0.001 HIS C 112 PHE 0.021 0.002 PHE A 256 TYR 0.018 0.001 TYR C 22 ARG 0.010 0.001 ARG A 326 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8898.10 seconds wall clock time: 157 minutes 28.04 seconds (9448.04 seconds total)