Starting phenix.real_space_refine on Wed Feb 14 22:47:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqt_13604/02_2024/7pqt_13604.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqt_13604/02_2024/7pqt_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqt_13604/02_2024/7pqt_13604.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqt_13604/02_2024/7pqt_13604.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqt_13604/02_2024/7pqt_13604.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqt_13604/02_2024/7pqt_13604.pdb" } 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 Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 380": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 10.10, per 1000 atoms: 0.97 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.28 Conformation dependent library (CDL) restraints added in 3.5 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: 1.07 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: 2.79 Time building geometry restraints manager: 4.58 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: 99.31 - 106.28: 289 106.28 - 113.24: 5714 113.24 - 120.21: 4376 120.21 - 127.18: 4123 127.18 - 134.14: 154 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 2.440 nonbonded pdb=" OD1 ASP B 97 " pdb=" OG1 THR B 99 " model vdw 2.166 2.440 nonbonded pdb=" OD1 ASP C 97 " pdb=" OG1 THR C 99 " model vdw 2.171 2.440 nonbonded pdb=" OE1 GLU C 98 " pdb=" OH TYR C 109 " model vdw 2.182 2.440 nonbonded pdb=" NH2 ARG B 33 " pdb=" O PHE B 93 " model vdw 2.191 2.520 ... (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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 112 or resid 114 through 240 or resid 242 throug \ h 367 or resid 369 through 448 or resid 450 through 453)) selection = (chain 'B' and (resid 7 through 112 or resid 114 through 240 or resid 242 throug \ h 367 or resid 369 through 448 or resid 450 through 453)) selection = (chain 'C' and (resid 7 through 112 or resid 114 through 240 or resid 242 throug \ h 367 or resid 369 through 448 or resid 450 through 453)) selection = (chain 'D' and (resid 7 through 112 or resid 114 through 240 or resid 242 throug \ h 367 or resid 369 through 448 or resid 450 through 453)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 9.010 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 37.270 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.070 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:12.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.320 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 99 poor density : 194 time to evaluate : 1.121 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: 0.8821 time to fit residues: 270.9633 Evaluate side-chains 233 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 178 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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: 0.7980 chunk 52 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 HIS D 45 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.1335 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= 0.222 Angle : 0.701 13.442 14656 Z= 0.353 Chirality : 0.043 0.179 1632 Planarity : 0.005 0.046 1828 Dihedral : 8.350 59.446 1503 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.23 % Favored : 94.28 % Rotamer: Outliers : 7.07 % Allowed : 30.34 % Favored : 62.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.21), residues: 1268 helix: -0.79 (0.17), residues: 804 sheet: None (None), residues: 0 loop : -1.99 (0.25), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 255 HIS 0.003 0.001 HIS A 112 PHE 0.022 0.002 PHE D 315 TYR 0.018 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 fitting. rotamer outliers: 62 poor density : 196 time to evaluate : 1.289 Fit side-chains revert: symmetry clash REVERT: A 89 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: A 450 GLN cc_start: 0.7123 (OUTLIER) cc_final: 0.6733 (mt0) REVERT: B 89 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7528 (tt0) REVERT: C 210 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.6488 (mp0) REVERT: C 380 GLU cc_start: 0.2963 (OUTLIER) cc_final: 0.2414 (mp0) outliers start: 62 outliers final: 23 residues processed: 238 average time/residue: 0.8973 time to fit residues: 235.0183 Evaluate side-chains 214 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 186 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 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 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 89 GLU 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 11 VAL Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 380 GLU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 412 SER 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 3.9990 chunk 34 optimal weight: 0.3980 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 111 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS D 45 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.1305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 10768 Z= 0.441 Angle : 0.759 14.487 14656 Z= 0.388 Chirality : 0.048 0.184 1632 Planarity : 0.006 0.045 1828 Dihedral : 7.237 58.733 1441 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.41 % Allowed : 6.37 % Favored : 93.22 % Rotamer: Outliers : 8.06 % Allowed : 29.98 % Favored : 61.96 % 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: -1.39 (0.22), residues: 1268 helix: -0.30 (0.18), residues: 760 sheet: -0.79 (0.70), residues: 40 loop : -1.87 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 255 HIS 0.003 0.001 HIS C 77 PHE 0.023 0.002 PHE A 260 TYR 0.021 0.002 TYR C 22 ARG 0.006 0.001 ARG D 59 *********************** 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 258 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 185 time to evaluate : 1.225 Fit side-chains revert: symmetry clash REVERT: A 450 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6733 (mt0) REVERT: B 89 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7559 (tt0) REVERT: B 350 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7912 (mt) REVERT: C 210 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.6496 (mp0) REVERT: D 23 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7259 (mtt180) REVERT: D 68 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.8195 (tt) REVERT: D 107 MET cc_start: 0.7212 (OUTLIER) cc_final: 0.6196 (mpp) REVERT: D 386 ASN cc_start: 0.7613 (OUTLIER) cc_final: 0.7158 (p0) outliers start: 73 outliers final: 32 residues processed: 235 average time/residue: 0.8392 time to fit residues: 218.1112 Evaluate side-chains 221 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 181 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 321 ILE Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 10 ILE Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 412 SER Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 338 LEU Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 412 SER Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 107 MET 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 341 SER Chi-restraints excluded: chain D residue 386 ASN Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 427 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 0.0970 chunk 32 optimal weight: 0.5980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 HIS D 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6824 moved from start: 0.1825 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 : 0.690 14.002 14656 Z= 0.338 Chirality : 0.042 0.176 1632 Planarity : 0.005 0.041 1828 Dihedral : 6.428 59.587 1437 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.74 % Favored : 94.93 % Rotamer: Outliers : 6.16 % Allowed : 31.52 % Favored : 62.32 % 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: -0.77 (0.23), residues: 1268 helix: 0.18 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.62 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 255 HIS 0.003 0.001 HIS A 112 PHE 0.017 0.001 PHE B 55 TYR 0.021 0.001 TYR C 48 ARG 0.010 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 250 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 198 time to evaluate : 1.209 Fit side-chains revert: symmetry clash REVERT: A 450 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6680 (mt0) REVERT: B 259 GLU cc_start: 0.5761 (OUTLIER) cc_final: 0.5512 (tt0) REVERT: C 210 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: D 107 MET cc_start: 0.7135 (OUTLIER) cc_final: 0.6289 (mpp) REVERT: D 341 SER cc_start: 0.8295 (m) cc_final: 0.8088 (p) REVERT: D 430 MET cc_start: 0.6300 (mmm) cc_final: 0.5023 (mtm) outliers start: 52 outliers final: 23 residues processed: 232 average time/residue: 0.9292 time to fit residues: 238.0418 Evaluate side-chains 212 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 262 MET 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 119 LEU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 259 GLU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 389 ILE 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 346 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 254 VAL Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 318 ILE Chi-restraints excluded: chain D residue 328 PHE Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 412 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 0.0980 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 HIS D 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.1829 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= 0.278 Angle : 0.715 15.540 14656 Z= 0.353 Chirality : 0.044 0.181 1632 Planarity : 0.005 0.041 1828 Dihedral : 6.223 58.174 1433 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.07 % Favored : 94.61 % Rotamer: Outliers : 6.70 % Allowed : 31.34 % Favored : 61.96 % 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: -0.68 (0.23), residues: 1268 helix: 0.26 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.58 (0.25), residues: 480 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 0.023 0.002 PHE A 260 TYR 0.018 0.001 TYR C 22 ARG 0.009 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 247 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 189 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 450 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.6692 (mt0) REVERT: C 210 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6436 (mp0) REVERT: D 107 MET cc_start: 0.7148 (OUTLIER) cc_final: 0.6205 (mpp) outliers start: 58 outliers final: 29 residues processed: 228 average time/residue: 0.8915 time to fit residues: 223.9417 Evaluate side-chains 211 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 179 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 262 MET 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 441 MET Chi-restraints excluded: chain A residue 450 GLN Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 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 346 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 11 VAL Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 254 VAL 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 412 SER Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 119 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 HIS D 111 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.2013 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= 0.238 Angle : 0.704 16.345 14656 Z= 0.343 Chirality : 0.044 0.182 1632 Planarity : 0.005 0.041 1828 Dihedral : 6.026 56.432 1433 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.98 % Favored : 94.69 % Rotamer: Outliers : 6.34 % Allowed : 31.61 % Favored : 62.05 % 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: 0.41 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.50 (0.25), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 255 HIS 0.003 0.001 HIS A 112 PHE 0.022 0.002 PHE B 55 TYR 0.030 0.001 TYR C 48 ARG 0.007 0.001 ARG A 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 232 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 178 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: C 210 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6424 (mp0) REVERT: D 107 MET cc_start: 0.7113 (OUTLIER) cc_final: 0.6235 (mpp) REVERT: D 380 GLU cc_start: 0.3618 (OUTLIER) cc_final: 0.2561 (mp0) REVERT: D 430 MET cc_start: 0.6287 (mmm) cc_final: 0.4817 (mtm) outliers start: 54 outliers final: 27 residues processed: 210 average time/residue: 0.9497 time to fit residues: 219.1619 Evaluate side-chains 207 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 177 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 262 MET Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 427 THR Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain C residue 21 THR Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 346 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 107 MET 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 380 GLU 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 115 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 0.1980 chunk 87 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 119 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 HIS D 45 HIS D 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10768 Z= 0.191 Angle : 0.699 16.154 14656 Z= 0.334 Chirality : 0.042 0.182 1632 Planarity : 0.005 0.056 1828 Dihedral : 5.470 53.883 1429 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.98 % Favored : 94.69 % Rotamer: Outliers : 5.62 % Allowed : 32.16 % Favored : 62.23 % 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: -0.19 (0.23), residues: 1268 helix: 0.60 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.29 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 255 HIS 0.003 0.001 HIS A 112 PHE 0.019 0.001 PHE D 315 TYR 0.018 0.001 TYR D 48 ARG 0.012 0.001 ARG C 314 *********************** 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 247 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 201 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 210 GLU cc_start: 0.6631 (OUTLIER) cc_final: 0.6371 (mp0) REVERT: D 107 MET cc_start: 0.7128 (OUTLIER) cc_final: 0.6284 (mpp) REVERT: D 430 MET cc_start: 0.6290 (mmm) cc_final: 0.4970 (mtm) outliers start: 46 outliers final: 24 residues processed: 223 average time/residue: 0.8134 time to fit residues: 201.4933 Evaluate side-chains 220 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 194 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 210 GLU Chi-restraints excluded: chain A residue 253 VAL Chi-restraints excluded: chain A residue 257 THR Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 209 LEU Chi-restraints excluded: chain D residue 258 PHE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 328 PHE Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 441 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 93 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS B 111 GLN C 13 ASN D 45 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10768 Z= 0.397 Angle : 0.765 14.732 14656 Z= 0.380 Chirality : 0.049 0.369 1632 Planarity : 0.006 0.082 1828 Dihedral : 5.377 52.907 1425 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.23 % Favored : 94.44 % Rotamer: Outliers : 4.89 % Allowed : 33.33 % Favored : 61.78 % 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: -0.38 (0.23), residues: 1268 helix: 0.49 (0.19), residues: 784 sheet: -0.29 (0.70), residues: 40 loop : -1.53 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 255 HIS 0.009 0.001 HIS C 112 PHE 0.018 0.002 PHE B 55 TYR 0.018 0.002 TYR C 22 ARG 0.014 0.001 ARG D 314 *********************** 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 222 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 184 time to evaluate : 1.301 Fit side-chains REVERT: C 210 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.6442 (mp0) REVERT: D 107 MET cc_start: 0.7153 (OUTLIER) cc_final: 0.6191 (mpp) REVERT: D 430 MET cc_start: 0.6401 (mmm) cc_final: 0.5029 (mtm) outliers start: 38 outliers final: 21 residues processed: 207 average time/residue: 0.8469 time to fit residues: 194.4728 Evaluate side-chains 205 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 182 time to evaluate : 1.161 ------------------------------------------------------------------------------- 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 389 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 264 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 48 optimal weight: 0.4980 chunk 87 optimal weight: 0.6980 chunk 34 optimal weight: 0.0040 chunk 100 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 0.5980 chunk 73 optimal weight: 0.3980 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 111 GLN D 45 HIS D 111 GLN D 216 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10768 Z= 0.198 Angle : 0.709 12.800 14656 Z= 0.343 Chirality : 0.044 0.320 1632 Planarity : 0.005 0.055 1828 Dihedral : 4.900 47.247 1423 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.66 % Favored : 95.02 % Rotamer: Outliers : 3.99 % Allowed : 33.97 % Favored : 62.05 % 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: -0.07 (0.24), residues: 1268 helix: 0.70 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.25 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 255 HIS 0.006 0.001 HIS C 112 PHE 0.023 0.002 PHE D 315 TYR 0.014 0.001 TYR C 22 ARG 0.013 0.001 ARG C 314 *********************** 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 217 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 189 time to evaluate : 1.195 Fit side-chains REVERT: A 209 LEU cc_start: 0.8068 (mm) cc_final: 0.7843 (mp) REVERT: C 210 GLU cc_start: 0.6648 (OUTLIER) cc_final: 0.6382 (mp0) REVERT: D 107 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6237 (mpp) REVERT: D 430 MET cc_start: 0.6267 (mmm) cc_final: 0.4893 (mtm) outliers start: 28 outliers final: 21 residues processed: 208 average time/residue: 0.8592 time to fit residues: 197.7774 Evaluate side-chains 204 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 181 time to evaluate : 1.209 ------------------------------------------------------------------------------- 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 389 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 264 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 81 optimal weight: 0.6980 chunk 123 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 0.5980 chunk 78 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6827 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10768 Z= 0.261 Angle : 0.743 13.024 14656 Z= 0.361 Chirality : 0.046 0.386 1632 Planarity : 0.005 0.102 1828 Dihedral : 4.932 41.817 1423 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.49 % Favored : 95.18 % Rotamer: Outliers : 3.80 % Allowed : 34.24 % Favored : 61.96 % 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: -0.07 (0.23), residues: 1268 helix: 0.69 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.24 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 255 HIS 0.007 0.001 HIS C 112 PHE 0.025 0.002 PHE D 55 TYR 0.014 0.001 TYR C 22 ARG 0.024 0.001 ARG D 314 ********************** 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 204 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 178 time to evaluate : 1.198 Fit side-chains REVERT: C 210 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.6411 (mp0) REVERT: D 107 MET cc_start: 0.7116 (OUTLIER) cc_final: 0.6209 (mpp) REVERT: D 430 MET cc_start: 0.6343 (mmm) cc_final: 0.4934 (mtm) outliers start: 26 outliers final: 21 residues processed: 195 average time/residue: 0.8794 time to fit residues: 189.3023 Evaluate side-chains 199 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 176 time to evaluate : 1.173 ------------------------------------------------------------------------------- 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 389 ILE Chi-restraints excluded: chain A residue 427 THR Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain B residue 321 ILE Chi-restraints excluded: chain B residue 350 ILE Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain C residue 111 GLN Chi-restraints excluded: chain C residue 210 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 324 LEU Chi-restraints excluded: chain C residue 427 THR Chi-restraints excluded: chain C residue 447 MET Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 389 ILE Chi-restraints excluded: chain D residue 412 SER Chi-restraints excluded: chain D residue 427 THR Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 447 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.130007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.098499 restraints weight = 99838.523| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 4.60 r_work: 0.3139 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10768 Z= 0.256 Angle : 0.740 15.397 14656 Z= 0.360 Chirality : 0.045 0.394 1632 Planarity : 0.005 0.097 1828 Dihedral : 4.921 37.383 1423 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.66 % Favored : 95.02 % Rotamer: Outliers : 3.71 % Allowed : 34.15 % Favored : 62.14 % 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 (0.23), residues: 1268 helix: 0.73 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.22 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 255 HIS 0.006 0.001 HIS C 112 PHE 0.021 0.002 PHE D 315 TYR 0.014 0.001 TYR C 22 ARG 0.021 0.001 ARG D 314 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4265.31 seconds wall clock time: 76 minutes 32.61 seconds (4592.61 seconds total)