Starting phenix.real_space_refine on Wed Nov 15 03:26:13 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqt_13604/11_2023/7pqt_13604.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqt_13604/11_2023/7pqt_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_13604/11_2023/7pqt_13604.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqt_13604/11_2023/7pqt_13604.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqt_13604/11_2023/7pqt_13604.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pqt_13604/11_2023/7pqt_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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 10.16, 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: 4.32 Conformation dependent library (CDL) restraints added in 3.3 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: 1.01 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: 3.02 Time building geometry restraints manager: 4.63 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: 3.250 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: 9.090 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 37.420 Find NCS groups from input model: 0.790 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:12.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.080 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.201 Fit side-chains outliers start: 99 outliers final: 46 residues processed: 278 average time/residue: 0.8749 time to fit residues: 268.0094 Evaluate side-chains 225 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 179 time to evaluate : 1.238 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 40 residues processed: 6 average time/residue: 0.1358 time to fit residues: 2.9802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 327 HIS B 66 HIS D 45 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6858 moved from start: 0.1270 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= 0.262 Angle : 0.717 14.343 14656 Z= 0.364 Chirality : 0.044 0.179 1632 Planarity : 0.005 0.046 1828 Dihedral : 5.289 24.748 1420 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.49 % Allowed : 5.72 % Favored : 93.79 % Rotamer: Outliers : 9.42 % Allowed : 28.89 % Favored : 61.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.21), residues: 1268 helix: -0.83 (0.17), residues: 804 sheet: None (None), residues: 0 loop : -2.00 (0.25), residues: 464 *********************** 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 281 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 193 time to evaluate : 1.140 Fit side-chains revert: symmetry clash outliers start: 88 outliers final: 51 residues processed: 259 average time/residue: 0.8632 time to fit residues: 247.0740 Evaluate side-chains 239 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 188 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 42 residues processed: 9 average time/residue: 0.5004 time to fit residues: 6.8944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0020 chunk 93 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 111 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- 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: 0.6871 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10768 Z= 0.307 Angle : 0.716 15.540 14656 Z= 0.360 Chirality : 0.045 0.178 1632 Planarity : 0.005 0.041 1828 Dihedral : 5.060 24.737 1420 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.21 % Favored : 93.46 % Rotamer: Outliers : 9.42 % Allowed : 28.17 % Favored : 62.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.22), residues: 1268 helix: -0.16 (0.18), residues: 784 sheet: -0.58 (0.71), residues: 40 loop : -1.84 (0.26), residues: 444 *********************** 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 283 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 195 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 88 outliers final: 51 residues processed: 262 average time/residue: 0.8238 time to fit residues: 239.2277 Evaluate side-chains 238 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 187 time to evaluate : 1.045 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 46 residues processed: 5 average time/residue: 0.1075 time to fit residues: 2.3282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 75 optimal weight: 0.0370 chunk 113 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 107 optimal weight: 0.2980 chunk 32 optimal weight: 0.9980 overall best weight: 0.5058 ------------------------------------------------------------------------------- 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: 0.6815 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10768 Z= 0.197 Angle : 0.671 13.938 14656 Z= 0.331 Chirality : 0.042 0.187 1632 Planarity : 0.005 0.039 1828 Dihedral : 4.770 25.147 1420 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.58 % Favored : 95.10 % Rotamer: Outliers : 8.61 % Allowed : 29.35 % 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: -0.67 (0.23), residues: 1268 helix: 0.25 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.54 (0.26), residues: 480 *********************** 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 279 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 200 time to evaluate : 1.215 Fit side-chains revert: symmetry clash outliers start: 79 outliers final: 51 residues processed: 262 average time/residue: 0.8708 time to fit residues: 252.5536 Evaluate side-chains 243 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 192 time to evaluate : 1.204 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 46 residues processed: 5 average time/residue: 1.0587 time to fit residues: 7.4818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 1 optimal weight: 2.9990 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 0 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 30 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: ** 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: 0.6881 moved from start: 0.1745 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= 0.368 Angle : 0.733 15.269 14656 Z= 0.369 Chirality : 0.047 0.447 1632 Planarity : 0.005 0.043 1828 Dihedral : 4.911 24.289 1420 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.23 % Favored : 94.44 % Rotamer: Outliers : 9.42 % Allowed : 29.17 % Favored : 61.41 % 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: -0.73 (0.23), residues: 1268 helix: 0.21 (0.19), residues: 784 sheet: -0.47 (0.70), residues: 40 loop : -1.65 (0.26), residues: 444 *********************** 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 275 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 187 time to evaluate : 1.282 Fit side-chains revert: symmetry clash outliers start: 88 outliers final: 55 residues processed: 254 average time/residue: 0.9579 time to fit residues: 269.3197 Evaluate side-chains 235 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 180 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 48 residues processed: 7 average time/residue: 0.7031 time to fit residues: 7.1321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 29 optimal weight: 0.4980 chunk 119 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.3980 chunk 62 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.6825 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10768 Z= 0.210 Angle : 0.696 16.041 14656 Z= 0.338 Chirality : 0.043 0.253 1632 Planarity : 0.005 0.040 1828 Dihedral : 4.711 24.908 1420 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.66 % Favored : 95.02 % Rotamer: Outliers : 7.70 % Allowed : 30.53 % 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: -0.44 (0.23), residues: 1268 helix: 0.40 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.40 (0.26), residues: 480 *********************** 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 258 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 189 time to evaluate : 1.133 Fit side-chains revert: symmetry clash outliers start: 69 outliers final: 51 residues processed: 248 average time/residue: 0.7947 time to fit residues: 219.7322 Evaluate side-chains 235 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 184 time to evaluate : 1.247 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 49 residues processed: 3 average time/residue: 1.4453 time to fit residues: 6.2001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 119 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10768 Z= 0.244 Angle : 0.713 16.338 14656 Z= 0.349 Chirality : 0.045 0.222 1632 Planarity : 0.005 0.040 1828 Dihedral : 4.693 24.674 1420 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.49 % Favored : 95.18 % Rotamer: Outliers : 7.61 % Allowed : 30.53 % Favored : 61.87 % 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: -0.36 (0.23), residues: 1268 helix: 0.45 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.33 (0.26), residues: 480 *********************** 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 263 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 195 time to evaluate : 1.183 Fit side-chains outliers start: 68 outliers final: 52 residues processed: 251 average time/residue: 0.8170 time to fit residues: 227.9917 Evaluate side-chains 242 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 190 time to evaluate : 1.172 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 47 residues processed: 5 average time/residue: 0.5666 time to fit residues: 4.8757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 0.1980 chunk 93 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- 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 D 111 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10768 Z= 0.368 Angle : 0.760 15.525 14656 Z= 0.375 Chirality : 0.047 0.331 1632 Planarity : 0.005 0.043 1828 Dihedral : 4.842 24.261 1420 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.23 % Favored : 94.44 % Rotamer: Outliers : 7.16 % Allowed : 30.71 % 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: -0.48 (0.23), residues: 1268 helix: 0.39 (0.19), residues: 784 sheet: -0.50 (0.69), residues: 40 loop : -1.50 (0.26), residues: 444 *********************** 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 248 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 185 time to evaluate : 1.241 Fit side-chains outliers start: 63 outliers final: 49 residues processed: 241 average time/residue: 0.8192 time to fit residues: 220.4006 Evaluate side-chains 230 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 181 time to evaluate : 1.089 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 46 residues processed: 4 average time/residue: 0.7721 time to fit residues: 4.8920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 111 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 48 optimal weight: 0.4980 chunk 87 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 73 optimal weight: 0.0570 overall best weight: 0.5298 ------------------------------------------------------------------------------- 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: 0.6815 moved from start: 0.2294 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= 0.208 Angle : 0.717 15.953 14656 Z= 0.347 Chirality : 0.043 0.232 1632 Planarity : 0.005 0.041 1828 Dihedral : 4.684 25.493 1420 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.82 % Favored : 94.85 % Rotamer: Outliers : 6.43 % Allowed : 30.98 % Favored : 62.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.24), residues: 1268 helix: 0.57 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.25 (0.26), residues: 480 *********************** 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 245 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 190 time to evaluate : 1.207 Fit side-chains outliers start: 55 outliers final: 45 residues processed: 239 average time/residue: 0.8405 time to fit residues: 224.6989 Evaluate side-chains 232 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 187 time to evaluate : 1.132 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 44 residues processed: 1 average time/residue: 0.0970 time to fit residues: 1.7024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.3980 chunk 71 optimal weight: 0.0010 chunk 55 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 D 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.2420 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= 0.210 Angle : 0.734 16.777 14656 Z= 0.352 Chirality : 0.044 0.344 1632 Planarity : 0.005 0.040 1828 Dihedral : 4.645 27.071 1420 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.90 % Favored : 94.77 % Rotamer: Outliers : 5.71 % Allowed : 31.70 % Favored : 62.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.24), residues: 1268 helix: 0.61 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.15 (0.27), residues: 480 ********************** 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 233 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 186 time to evaluate : 1.269 Fit side-chains outliers start: 47 outliers final: 47 residues processed: 231 average time/residue: 0.7851 time to fit residues: 202.4384 Evaluate side-chains 228 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 181 time to evaluate : 1.186 Switching outliers to nearest non-outliers outliers start: 47 outliers final: 46 residues processed: 1 average time/residue: 1.0453 time to fit residues: 2.7258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 90 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 41 optimal weight: 0.3980 chunk 101 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 chunk 86 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 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 = 0.3796 r_free = 0.3796 target = 0.132042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.100204 restraints weight = 98971.619| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 4.57 r_work: 0.3162 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 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 = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10768 Z= 0.214 Angle : 0.722 16.521 14656 Z= 0.350 Chirality : 0.044 0.293 1632 Planarity : 0.005 0.046 1828 Dihedral : 4.644 29.694 1420 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.33 % Allowed : 5.07 % Favored : 94.61 % Rotamer: Outliers : 5.80 % Allowed : 32.07 % 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: -0.06 (0.24), residues: 1268 helix: 0.65 (0.19), residues: 788 sheet: None (None), residues: 0 loop : -1.12 (0.27), residues: 480 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4445.08 seconds wall clock time: 79 minutes 44.50 seconds (4784.50 seconds total)