Starting phenix.real_space_refine on Mon Mar 11 00:59:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6k_32328/03_2024/7w6k_32328.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6k_32328/03_2024/7w6k_32328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6k_32328/03_2024/7w6k_32328.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6k_32328/03_2024/7w6k_32328.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6k_32328/03_2024/7w6k_32328.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w6k_32328/03_2024/7w6k_32328.pdb" } resolution = 3.5 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= 0.041 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: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 4202 2.51 5 N 1094 2.21 5 O 1142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 198": "NH1" <-> "NH2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 251": "OE1" <-> "OE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 274": "OD1" <-> "OD2" Residue "A ASP 279": "OD1" <-> "OD2" Residue "A ARG 291": "NH1" <-> "NH2" Residue "A TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 298": "NH1" <-> "NH2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 326": "NH1" <-> "NH2" Residue "A GLU 328": "OE1" <-> "OE2" Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A ASP 382": "OD1" <-> "OD2" Residue "A GLU 472": "OE1" <-> "OE2" Residue "A PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 491": "OD1" <-> "OD2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 178": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 198": "NH1" <-> "NH2" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B PHE 248": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 251": "OE1" <-> "OE2" Residue "B TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 274": "OD1" <-> "OD2" Residue "B ASP 279": "OD1" <-> "OD2" Residue "B ARG 291": "NH1" <-> "NH2" Residue "B TYR 295": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 298": "NH1" <-> "NH2" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 326": "NH1" <-> "NH2" Residue "B GLU 328": "OE1" <-> "OE2" Residue "B PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 378": "OE1" <-> "OE2" Residue "B ASP 382": "OD1" <-> "OD2" Residue "B GLU 472": "OE1" <-> "OE2" Residue "B PHE 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 479": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 491": "OD1" <-> "OD2" Residue "B GLU 495": "OE1" <-> "OE2" Residue "B ARG 502": "NH1" <-> "NH2" Residue "B PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6468 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3234 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 14, 'TRANS': 395} Chain breaks: 1 Chain: "B" Number of atoms: 3234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 410, 3234 Classifications: {'peptide': 410} Link IDs: {'PTRANS': 14, 'TRANS': 395} Chain breaks: 1 Time building chain proxies: 4.11, per 1000 atoms: 0.64 Number of scatterers: 6468 At special positions: 0 Unit cell: (74.88, 92.56, 107.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 30 16.00 O 1142 8.00 N 1094 7.00 C 4202 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: 2.51 Conformation dependent library (CDL) restraints added in 1.3 seconds 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1544 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 0 sheets defined 82.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 37 through 54 removed outlier: 4.668A pdb=" N ASN A 41 " --> pdb=" O MET A 37 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP A 44 " --> pdb=" O PRO A 40 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 73 Processing helix chain 'A' and resid 73 through 78 removed outlier: 3.578A pdb=" N LEU A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 73 through 78' Processing helix chain 'A' and resid 80 through 86 removed outlier: 4.036A pdb=" N ILE A 84 " --> pdb=" O PHE A 81 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N GLY A 85 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLN A 86 " --> pdb=" O GLY A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 99 removed outlier: 4.137A pdb=" N ALA A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 131 removed outlier: 4.097A pdb=" N GLY A 110 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 160 Processing helix chain 'A' and resid 160 through 165 removed outlier: 4.614A pdb=" N LYS A 165 " --> pdb=" O PRO A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 188 removed outlier: 3.632A pdb=" N PHE A 174 " --> pdb=" O GLY A 170 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR A 186 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG A 187 " --> pdb=" O VAL A 183 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 215 removed outlier: 3.864A pdb=" N LYS A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N TYR A 200 " --> pdb=" O HIS A 196 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 249 Processing helix chain 'A' and resid 259 through 262 Processing helix chain 'A' and resid 263 through 288 removed outlier: 4.775A pdb=" N ALA A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LYS A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 7.399A pdb=" N SER A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE A 278 " --> pdb=" O ASP A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 325 Processing helix chain 'A' and resid 332 through 338 removed outlier: 3.911A pdb=" N MET A 338 " --> pdb=" O SER A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 363 removed outlier: 3.776A pdb=" N ILE A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 389 Processing helix chain 'A' and resid 459 through 468 removed outlier: 3.812A pdb=" N ILE A 463 " --> pdb=" O GLN A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 504 removed outlier: 4.012A pdb=" N ASP A 491 " --> pdb=" O VAL A 487 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 54 removed outlier: 4.668A pdb=" N ASN B 41 " --> pdb=" O MET B 37 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP B 44 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN B 45 " --> pdb=" O ASN B 41 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 54 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 73 Processing helix chain 'B' and resid 73 through 78 removed outlier: 3.578A pdb=" N LEU B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 73 through 78' Processing helix chain 'B' and resid 80 through 86 removed outlier: 4.037A pdb=" N ILE B 84 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLY B 85 " --> pdb=" O LYS B 82 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N GLN B 86 " --> pdb=" O GLY B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 99 removed outlier: 4.137A pdb=" N ALA B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 131 removed outlier: 4.096A pdb=" N GLY B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 160 Processing helix chain 'B' and resid 160 through 165 removed outlier: 4.614A pdb=" N LYS B 165 " --> pdb=" O PRO B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 188 removed outlier: 3.632A pdb=" N PHE B 174 " --> pdb=" O GLY B 170 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER B 184 " --> pdb=" O LEU B 180 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N TYR B 186 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ARG B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 215 removed outlier: 3.864A pdb=" N LYS B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N TYR B 200 " --> pdb=" O HIS B 196 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 249 Processing helix chain 'B' and resid 259 through 262 Processing helix chain 'B' and resid 263 through 288 removed outlier: 4.775A pdb=" N ALA B 271 " --> pdb=" O LYS B 267 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N LYS B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N SER B 277 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ILE B 278 " --> pdb=" O ASP B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 325 Processing helix chain 'B' and resid 332 through 338 removed outlier: 3.910A pdb=" N MET B 338 " --> pdb=" O SER B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 363 removed outlier: 3.776A pdb=" N ILE B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG B 345 " --> pdb=" O ASP B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 389 Processing helix chain 'B' and resid 459 through 468 removed outlier: 3.812A pdb=" N ILE B 463 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 473 through 504 removed outlier: 4.012A pdb=" N ASP B 491 " --> pdb=" O VAL B 487 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 492 " --> pdb=" O ALA B 488 " (cutoff:3.500A) 466 hydrogen bonds defined for protein. 1386 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: 2.42 Time building geometry restraints manager: 2.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1300 1.33 - 1.45: 1511 1.45 - 1.57: 3755 1.57 - 1.69: 0 1.69 - 1.82: 42 Bond restraints: 6608 Sorted by residual: bond pdb=" CA SER B 358 " pdb=" CB SER B 358 " ideal model delta sigma weight residual 1.528 1.466 0.063 1.56e-02 4.11e+03 1.62e+01 bond pdb=" CA SER A 358 " pdb=" CB SER A 358 " ideal model delta sigma weight residual 1.528 1.466 0.063 1.56e-02 4.11e+03 1.61e+01 bond pdb=" CA SER B 360 " pdb=" CB SER B 360 " ideal model delta sigma weight residual 1.529 1.470 0.059 1.58e-02 4.01e+03 1.40e+01 bond pdb=" N PRO A 369 " pdb=" CD PRO A 369 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.39e+01 bond pdb=" N PRO B 369 " pdb=" CD PRO B 369 " ideal model delta sigma weight residual 1.473 1.525 -0.052 1.40e-02 5.10e+03 1.39e+01 ... (remaining 6603 not shown) Histogram of bond angle deviations from ideal: 99.46 - 106.43: 183 106.43 - 113.40: 3640 113.40 - 120.38: 2874 120.38 - 127.35: 2198 127.35 - 134.33: 67 Bond angle restraints: 8962 Sorted by residual: angle pdb=" N ILE B 252 " pdb=" CA ILE B 252 " pdb=" C ILE B 252 " ideal model delta sigma weight residual 108.35 99.46 8.89 1.32e+00 5.74e-01 4.54e+01 angle pdb=" N ILE A 252 " pdb=" CA ILE A 252 " pdb=" C ILE A 252 " ideal model delta sigma weight residual 108.35 99.46 8.89 1.32e+00 5.74e-01 4.53e+01 angle pdb=" N PHE B 470 " pdb=" CA PHE B 470 " pdb=" C PHE B 470 " ideal model delta sigma weight residual 110.23 100.99 9.24 1.45e+00 4.76e-01 4.06e+01 angle pdb=" N PHE A 470 " pdb=" CA PHE A 470 " pdb=" C PHE A 470 " ideal model delta sigma weight residual 110.23 100.99 9.24 1.45e+00 4.76e-01 4.06e+01 angle pdb=" N GLY A 114 " pdb=" CA GLY A 114 " pdb=" C GLY A 114 " ideal model delta sigma weight residual 112.50 119.17 -6.67 1.16e+00 7.43e-01 3.30e+01 ... (remaining 8957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 3484 17.73 - 35.45: 374 35.45 - 53.18: 68 53.18 - 70.90: 6 70.90 - 88.63: 4 Dihedral angle restraints: 3936 sinusoidal: 1542 harmonic: 2394 Sorted by residual: dihedral pdb=" C PHE B 248 " pdb=" N PHE B 248 " pdb=" CA PHE B 248 " pdb=" CB PHE B 248 " ideal model delta harmonic sigma weight residual -122.60 -134.88 12.28 0 2.50e+00 1.60e-01 2.41e+01 dihedral pdb=" C PHE A 248 " pdb=" N PHE A 248 " pdb=" CA PHE A 248 " pdb=" CB PHE A 248 " ideal model delta harmonic sigma weight residual -122.60 -134.86 12.26 0 2.50e+00 1.60e-01 2.40e+01 dihedral pdb=" C TYR A 257 " pdb=" N TYR A 257 " pdb=" CA TYR A 257 " pdb=" CB TYR A 257 " ideal model delta harmonic sigma weight residual -122.60 -134.00 11.40 0 2.50e+00 1.60e-01 2.08e+01 ... (remaining 3933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 924 0.086 - 0.172: 78 0.172 - 0.259: 30 0.259 - 0.345: 8 0.345 - 0.431: 4 Chirality restraints: 1044 Sorted by residual: chirality pdb=" CA PHE B 248 " pdb=" N PHE B 248 " pdb=" C PHE B 248 " pdb=" CB PHE B 248 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA PHE A 248 " pdb=" N PHE A 248 " pdb=" C PHE A 248 " pdb=" CB PHE A 248 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA TYR A 257 " pdb=" N TYR A 257 " pdb=" C TYR A 257 " pdb=" CB TYR A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.04e+00 ... (remaining 1041 not shown) Planarity restraints: 1112 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PRO A 161 " 0.020 2.00e-02 2.50e+03 4.07e-02 1.65e+01 pdb=" C PRO A 161 " -0.070 2.00e-02 2.50e+03 pdb=" O PRO A 161 " 0.026 2.00e-02 2.50e+03 pdb=" N TYR A 162 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO B 161 " 0.020 2.00e-02 2.50e+03 4.06e-02 1.65e+01 pdb=" C PRO B 161 " -0.070 2.00e-02 2.50e+03 pdb=" O PRO B 161 " 0.026 2.00e-02 2.50e+03 pdb=" N TYR B 162 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 163 " -0.018 2.00e-02 2.50e+03 3.66e-02 1.34e+01 pdb=" C ILE B 163 " 0.063 2.00e-02 2.50e+03 pdb=" O ILE B 163 " -0.023 2.00e-02 2.50e+03 pdb=" N LYS B 164 " -0.022 2.00e-02 2.50e+03 ... (remaining 1109 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 2519 2.85 - 3.36: 7355 3.36 - 3.87: 10787 3.87 - 4.39: 12544 4.39 - 4.90: 19461 Nonbonded interactions: 52666 Sorted by model distance: nonbonded pdb=" N SER A 221 " pdb=" OE2 GLU A 289 " model vdw 2.337 2.520 nonbonded pdb=" N SER B 221 " pdb=" OE2 GLU B 289 " model vdw 2.338 2.520 nonbonded pdb=" OD1 ASP A 135 " pdb=" OG SER A 138 " model vdw 2.360 2.440 nonbonded pdb=" OD1 ASP B 135 " pdb=" OG SER B 138 " model vdw 2.360 2.440 nonbonded pdb=" NZ LYS B 232 " pdb=" OD1 ASP B 279 " model vdw 2.366 2.520 ... (remaining 52661 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' selection = chain 'B' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.170 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: 0.000 Extract box with map and model: 2.720 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 23.340 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 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 : 0.007 0.063 6608 Z= 0.479 Angle : 1.134 9.238 8962 Z= 0.794 Chirality : 0.069 0.431 1044 Planarity : 0.006 0.041 1112 Dihedral : 14.610 88.630 2392 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 47.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.01 % Allowed : 10.06 % Favored : 87.93 % Cbeta Deviations : 0.52 % 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: -3.58 (0.24), residues: 812 helix: -1.77 (0.18), residues: 610 sheet: None (None), residues: 0 loop : -3.84 (0.34), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 44 HIS 0.010 0.002 HIS A 226 PHE 0.040 0.003 PHE A 248 TYR 0.020 0.002 TYR A 247 ARG 0.005 0.001 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 PHE cc_start: 0.8116 (t80) cc_final: 0.7916 (t80) REVERT: B 77 LEU cc_start: 0.8760 (pp) cc_final: 0.8544 (tt) outliers start: 14 outliers final: 0 residues processed: 187 average time/residue: 0.2139 time to fit residues: 52.1323 Evaluate side-chains 110 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 74 optimal weight: 0.0770 overall best weight: 1.1540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN A 132 ASN A 179 ASN A 219 ASN A 330 GLN A 377 HIS A 384 ASN A 390 GLN B 86 GLN B 132 ASN B 219 ASN B 330 GLN B 377 HIS B 390 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.3247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 6608 Z= 0.299 Angle : 0.796 8.454 8962 Z= 0.406 Chirality : 0.045 0.224 1044 Planarity : 0.005 0.062 1112 Dihedral : 5.416 20.387 896 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 4.45 % Allowed : 19.40 % Favored : 76.15 % 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: -1.52 (0.28), residues: 812 helix: -0.46 (0.19), residues: 628 sheet: None (None), residues: 0 loop : -2.57 (0.46), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 44 HIS 0.016 0.002 HIS A 322 PHE 0.025 0.002 PHE A 248 TYR 0.024 0.002 TYR A 269 ARG 0.007 0.001 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 PHE cc_start: 0.8486 (OUTLIER) cc_final: 0.8233 (t80) REVERT: A 243 CYS cc_start: 0.7361 (t) cc_final: 0.6852 (t) REVERT: A 322 HIS cc_start: 0.6826 (m90) cc_final: 0.6601 (m90) REVERT: A 375 HIS cc_start: 0.8507 (m90) cc_final: 0.8144 (m90) REVERT: B 125 PHE cc_start: 0.8553 (OUTLIER) cc_final: 0.8289 (t80) REVERT: B 375 HIS cc_start: 0.8548 (m90) cc_final: 0.8234 (m90) REVERT: B 481 SER cc_start: 0.7213 (m) cc_final: 0.6625 (m) outliers start: 31 outliers final: 17 residues processed: 154 average time/residue: 0.1472 time to fit residues: 31.9437 Evaluate side-chains 117 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 98 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 94 THR Chi-restraints excluded: chain B residue 125 PHE Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 493 VAL Chi-restraints excluded: chain B residue 494 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 30.0000 chunk 23 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 66 optimal weight: 0.2980 chunk 73 optimal weight: 0.6980 chunk 25 optimal weight: 0.3980 chunk 59 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6608 Z= 0.218 Angle : 0.690 10.088 8962 Z= 0.343 Chirality : 0.041 0.219 1044 Planarity : 0.004 0.036 1112 Dihedral : 5.091 22.380 896 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.46 % Allowed : 21.41 % Favored : 73.13 % 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: -0.27 (0.29), residues: 812 helix: 0.45 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.32 (0.46), residues: 174 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 44 HIS 0.009 0.001 HIS B 322 PHE 0.028 0.002 PHE A 248 TYR 0.026 0.002 TYR B 75 ARG 0.004 0.001 ARG B 113 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 116 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8831 (mm) cc_final: 0.8527 (tp) REVERT: A 125 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.8288 (t80) REVERT: A 375 HIS cc_start: 0.8428 (m90) cc_final: 0.8178 (m90) REVERT: B 247 TYR cc_start: 0.8545 (t80) cc_final: 0.8142 (t80) REVERT: B 375 HIS cc_start: 0.8386 (m90) cc_final: 0.8146 (m90) REVERT: B 486 THR cc_start: 0.9049 (OUTLIER) cc_final: 0.8848 (p) outliers start: 38 outliers final: 18 residues processed: 144 average time/residue: 0.1374 time to fit residues: 28.5098 Evaluate side-chains 114 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 94 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 493 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 486 THR Chi-restraints excluded: chain B residue 505 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 8.9990 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 9.9990 chunk 50 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN B 384 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6608 Z= 0.278 Angle : 0.680 9.213 8962 Z= 0.348 Chirality : 0.042 0.228 1044 Planarity : 0.005 0.036 1112 Dihedral : 4.876 20.241 896 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 6.18 % Allowed : 22.56 % Favored : 71.26 % 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: 0.16 (0.30), residues: 812 helix: 0.71 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -1.98 (0.48), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 44 HIS 0.012 0.001 HIS B 322 PHE 0.040 0.002 PHE B 248 TYR 0.027 0.002 TYR B 75 ARG 0.005 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 97 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8884 (mm) cc_final: 0.8564 (tp) REVERT: A 125 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.8310 (t80) REVERT: A 375 HIS cc_start: 0.8420 (m90) cc_final: 0.8178 (m90) REVERT: A 474 LEU cc_start: 0.8886 (tt) cc_final: 0.8685 (tp) REVERT: A 500 LEU cc_start: 0.8486 (tp) cc_final: 0.8275 (tt) REVERT: B 375 HIS cc_start: 0.8479 (m90) cc_final: 0.8180 (m90) outliers start: 43 outliers final: 33 residues processed: 124 average time/residue: 0.1315 time to fit residues: 24.0110 Evaluate side-chains 120 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 86 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 494 ILE Chi-restraints excluded: chain B residue 505 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 67 optimal weight: 0.0870 chunk 54 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.2962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 ASN ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.5195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6608 Z= 0.227 Angle : 0.687 11.775 8962 Z= 0.339 Chirality : 0.043 0.456 1044 Planarity : 0.004 0.034 1112 Dihedral : 4.798 19.206 896 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.46 % Allowed : 24.43 % Favored : 70.11 % 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: 0.45 (0.30), residues: 812 helix: 0.87 (0.20), residues: 644 sheet: None (None), residues: 0 loop : -1.75 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 44 HIS 0.010 0.001 HIS B 322 PHE 0.043 0.002 PHE B 248 TYR 0.028 0.002 TYR B 75 ARG 0.005 0.000 ARG B 298 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 99 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8873 (mm) cc_final: 0.8569 (tp) REVERT: A 125 PHE cc_start: 0.8530 (OUTLIER) cc_final: 0.8294 (t80) REVERT: A 375 HIS cc_start: 0.8415 (m90) cc_final: 0.8149 (m90) REVERT: A 500 LEU cc_start: 0.8454 (tp) cc_final: 0.8245 (tt) REVERT: B 375 HIS cc_start: 0.8447 (m90) cc_final: 0.8126 (m90) outliers start: 38 outliers final: 30 residues processed: 123 average time/residue: 0.1280 time to fit residues: 23.1169 Evaluate side-chains 108 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 77 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 125 PHE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 311 LEU Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 338 MET Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 494 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 36 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 20.0000 chunk 76 optimal weight: 0.0060 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.5542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6608 Z= 0.183 Angle : 0.658 10.416 8962 Z= 0.327 Chirality : 0.040 0.151 1044 Planarity : 0.004 0.034 1112 Dihedral : 4.684 20.414 896 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 5.03 % Allowed : 25.29 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.30), residues: 812 helix: 1.06 (0.21), residues: 644 sheet: None (None), residues: 0 loop : -1.80 (0.50), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 301 HIS 0.006 0.001 HIS A 322 PHE 0.022 0.002 PHE B 148 TYR 0.026 0.002 TYR B 75 ARG 0.003 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 93 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8909 (mm) cc_final: 0.8592 (tp) REVERT: A 196 HIS cc_start: 0.4358 (OUTLIER) cc_final: 0.3946 (t-90) REVERT: A 375 HIS cc_start: 0.8389 (m90) cc_final: 0.8122 (m90) REVERT: B 77 LEU cc_start: 0.8879 (mm) cc_final: 0.8546 (tt) REVERT: B 375 HIS cc_start: 0.8458 (m90) cc_final: 0.8154 (m90) outliers start: 35 outliers final: 28 residues processed: 117 average time/residue: 0.1565 time to fit residues: 27.6374 Evaluate side-chains 103 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 74 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 196 HIS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 209 CYS Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 262 GLU Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 299 PHE Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 494 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 3.9990 chunk 45 optimal weight: 0.4980 chunk 57 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 179 ASN ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6608 Z= 0.187 Angle : 0.642 10.533 8962 Z= 0.323 Chirality : 0.040 0.152 1044 Planarity : 0.004 0.034 1112 Dihedral : 4.631 21.460 896 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.74 % Allowed : 24.71 % Favored : 70.55 % 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: 0.76 (0.30), residues: 812 helix: 1.16 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -2.05 (0.49), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 301 HIS 0.008 0.001 HIS B 322 PHE 0.022 0.002 PHE A 248 TYR 0.027 0.002 TYR B 75 ARG 0.003 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 80 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8914 (mm) cc_final: 0.8602 (tp) REVERT: A 375 HIS cc_start: 0.8389 (m90) cc_final: 0.8117 (m90) REVERT: B 77 LEU cc_start: 0.8868 (mm) cc_final: 0.8529 (tt) REVERT: B 258 MET cc_start: 0.7750 (tmm) cc_final: 0.7547 (tmm) REVERT: B 375 HIS cc_start: 0.8468 (m90) cc_final: 0.8202 (m90) outliers start: 33 outliers final: 27 residues processed: 101 average time/residue: 0.1220 time to fit residues: 18.4893 Evaluate side-chains 101 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 74 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 494 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 50 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 73 optimal weight: 0.6980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6608 Z= 0.200 Angle : 0.638 9.444 8962 Z= 0.320 Chirality : 0.039 0.174 1044 Planarity : 0.004 0.034 1112 Dihedral : 4.545 19.483 896 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.74 % Allowed : 25.43 % Favored : 69.83 % 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: 0.96 (0.30), residues: 812 helix: 1.27 (0.21), residues: 650 sheet: None (None), residues: 0 loop : -1.90 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 301 HIS 0.011 0.001 HIS A 322 PHE 0.027 0.002 PHE B 479 TYR 0.028 0.002 TYR B 75 ARG 0.003 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 85 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8905 (mm) cc_final: 0.8582 (tp) REVERT: A 375 HIS cc_start: 0.8402 (m90) cc_final: 0.8116 (m90) REVERT: B 77 LEU cc_start: 0.8904 (mm) cc_final: 0.8567 (tt) REVERT: B 375 HIS cc_start: 0.8474 (m90) cc_final: 0.8196 (m90) outliers start: 33 outliers final: 28 residues processed: 106 average time/residue: 0.1326 time to fit residues: 20.7252 Evaluate side-chains 105 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 77 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 322 HIS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 262 GLU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 494 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 8.9990 chunk 22 optimal weight: 0.0270 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 overall best weight: 2.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 GLN ** A 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.6137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 6608 Z= 0.308 Angle : 0.693 8.206 8962 Z= 0.358 Chirality : 0.041 0.166 1044 Planarity : 0.005 0.036 1112 Dihedral : 4.636 21.748 896 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 4.17 % Allowed : 26.44 % Favored : 69.40 % 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: 0.88 (0.30), residues: 812 helix: 1.21 (0.21), residues: 650 sheet: None (None), residues: 0 loop : -1.92 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 301 HIS 0.007 0.001 HIS A 377 PHE 0.028 0.002 PHE B 148 TYR 0.025 0.002 TYR B 75 ARG 0.004 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 72 time to evaluate : 0.696 Fit side-chains REVERT: A 375 HIS cc_start: 0.8465 (m90) cc_final: 0.8109 (m90) REVERT: B 77 LEU cc_start: 0.8931 (mm) cc_final: 0.8625 (tt) REVERT: B 375 HIS cc_start: 0.8508 (m90) cc_final: 0.8209 (m90) outliers start: 29 outliers final: 25 residues processed: 92 average time/residue: 0.1278 time to fit residues: 17.6031 Evaluate side-chains 97 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 72 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 311 LEU Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 494 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.3980 chunk 54 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 75 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 GLN A 384 ASN ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.6433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6608 Z= 0.181 Angle : 0.659 9.829 8962 Z= 0.330 Chirality : 0.040 0.195 1044 Planarity : 0.004 0.034 1112 Dihedral : 4.613 19.696 896 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.45 % Allowed : 27.16 % Favored : 69.40 % 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: 1.15 (0.30), residues: 812 helix: 1.40 (0.21), residues: 650 sheet: None (None), residues: 0 loop : -1.79 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 44 HIS 0.007 0.001 HIS A 377 PHE 0.015 0.001 PHE A 476 TYR 0.029 0.001 TYR B 75 ARG 0.005 0.000 ARG A 294 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1624 Ramachandran restraints generated. 812 Oldfield, 0 Emsley, 812 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 76 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 115 LEU cc_start: 0.8858 (mm) cc_final: 0.8529 (tp) REVERT: A 375 HIS cc_start: 0.8402 (m90) cc_final: 0.8108 (m90) REVERT: B 77 LEU cc_start: 0.8897 (mm) cc_final: 0.8607 (tt) REVERT: B 279 ASP cc_start: 0.7713 (t70) cc_final: 0.7454 (t70) REVERT: B 375 HIS cc_start: 0.8462 (m90) cc_final: 0.8194 (m90) outliers start: 24 outliers final: 21 residues processed: 92 average time/residue: 0.1265 time to fit residues: 17.8038 Evaluate side-chains 93 residues out of total 696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 ILE Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 206 CYS Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 481 SER Chi-restraints excluded: chain A residue 494 ILE Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 75 TYR Chi-restraints excluded: chain B residue 102 THR Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 201 THR Chi-restraints excluded: chain B residue 209 CYS Chi-restraints excluded: chain B residue 324 CYS Chi-restraints excluded: chain B residue 341 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 481 SER Chi-restraints excluded: chain B residue 494 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 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 303 GLN A 384 ASN ** B 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.093335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.070422 restraints weight = 18851.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.073180 restraints weight = 10699.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.074945 restraints weight = 7406.093| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.6556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6608 Z= 0.187 Angle : 0.637 9.237 8962 Z= 0.325 Chirality : 0.040 0.177 1044 Planarity : 0.004 0.034 1112 Dihedral : 4.579 20.070 896 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 3.45 % Allowed : 27.44 % Favored : 69.11 % 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: 1.23 (0.30), residues: 812 helix: 1.47 (0.21), residues: 648 sheet: None (None), residues: 0 loop : -1.82 (0.48), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 301 HIS 0.010 0.001 HIS B 377 PHE 0.015 0.001 PHE A 476 TYR 0.028 0.001 TYR B 75 ARG 0.003 0.000 ARG A 294 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1505.48 seconds wall clock time: 29 minutes 5.99 seconds (1745.99 seconds total)