Starting phenix.real_space_refine on Thu Mar 5 09:42:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t20_25607/03_2026/7t20_25607.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t20_25607/03_2026/7t20_25607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t20_25607/03_2026/7t20_25607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t20_25607/03_2026/7t20_25607.map" model { file = "/net/cci-nas-00/data/ceres_data/7t20_25607/03_2026/7t20_25607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t20_25607/03_2026/7t20_25607.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians P 22 5.49 5 Mg 4 5.21 5 S 78 5.16 5 C 13028 2.51 5 N 3752 2.21 5 O 4222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21106 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3434 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 17, 'TRANS': 422} Chain: "B" Number of atoms: 3492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3492 Classifications: {'peptide': 447} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 428} Chain: "C" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3434 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 17, 'TRANS': 422} Chain: "D" Number of atoms: 3492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3492 Classifications: {'peptide': 447} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 428} Chain: "E" Number of atoms: 3434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3434 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 17, 'TRANS': 422} Chain: "F" Number of atoms: 3492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3492 Classifications: {'peptide': 447} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 428} Chain: "M" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 200 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.99, per 1000 atoms: 0.24 Number of scatterers: 21106 At special positions: 0 Unit cell: (118.08, 139.2, 137.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 78 16.00 P 22 15.00 Mg 4 11.99 O 4222 8.00 N 3752 7.00 C 13028 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 932.4 milliseconds 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4992 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 7 sheets defined 61.1% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.64 Creating SS restraints... Processing helix chain 'A' and resid 30 through 44 Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 56 through 60 Processing helix chain 'A' and resid 62 through 78 Processing helix chain 'A' and resid 83 through 94 Processing helix chain 'A' and resid 96 through 101 removed outlier: 3.740A pdb=" N GLY A 101 " --> pdb=" O LEU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 113 removed outlier: 3.670A pdb=" N THR A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 148 Processing helix chain 'A' and resid 153 through 172 Processing helix chain 'A' and resid 182 through 198 Processing helix chain 'A' and resid 211 through 217 Processing helix chain 'A' and resid 236 through 250 Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 280 through 286 Processing helix chain 'A' and resid 290 through 308 Processing helix chain 'A' and resid 319 through 334 Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.862A pdb=" N MET A 348 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 376 removed outlier: 4.336A pdb=" N GLU A 360 " --> pdb=" O ASN A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.505A pdb=" N LEU A 389 " --> pdb=" O ASN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 420 through 425 removed outlier: 3.542A pdb=" N TYR A 424 " --> pdb=" O ARG A 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 44 Processing helix chain 'B' and resid 47 through 55 removed outlier: 3.605A pdb=" N VAL B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 62 through 78 Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'B' and resid 96 through 101 removed outlier: 3.550A pdb=" N GLY B 101 " --> pdb=" O LEU B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 113 removed outlier: 3.686A pdb=" N THR B 113 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 148 Processing helix chain 'B' and resid 153 through 171 Processing helix chain 'B' and resid 182 through 199 Processing helix chain 'B' and resid 213 through 218 Processing helix chain 'B' and resid 236 through 252 Processing helix chain 'B' and resid 264 through 278 Processing helix chain 'B' and resid 280 through 287 Processing helix chain 'B' and resid 290 through 308 Processing helix chain 'B' and resid 319 through 335 Processing helix chain 'B' and resid 344 through 348 removed outlier: 3.501A pdb=" N LEU B 347 " --> pdb=" O TYR B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 376 Processing helix chain 'B' and resid 387 through 392 removed outlier: 3.554A pdb=" N GLN B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 412 removed outlier: 4.336A pdb=" N GLN B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 425 Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 47 through 55 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 62 through 78 Processing helix chain 'C' and resid 83 through 94 Processing helix chain 'C' and resid 96 through 101 removed outlier: 3.805A pdb=" N GLY C 101 " --> pdb=" O LEU C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 113 removed outlier: 3.737A pdb=" N THR C 113 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 148 Processing helix chain 'C' and resid 153 through 173 Processing helix chain 'C' and resid 182 through 199 Processing helix chain 'C' and resid 213 through 218 Processing helix chain 'C' and resid 236 through 251 Processing helix chain 'C' and resid 264 through 278 Processing helix chain 'C' and resid 280 through 287 removed outlier: 3.517A pdb=" N ILE C 284 " --> pdb=" O ASP C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 308 Processing helix chain 'C' and resid 319 through 335 Processing helix chain 'C' and resid 344 through 348 Processing helix chain 'C' and resid 356 through 376 Processing helix chain 'C' and resid 387 through 392 Processing helix chain 'C' and resid 406 through 412 Processing helix chain 'C' and resid 420 through 425 removed outlier: 3.666A pdb=" N TYR C 424 " --> pdb=" O ARG C 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 44 Processing helix chain 'D' and resid 47 through 55 Processing helix chain 'D' and resid 56 through 60 Processing helix chain 'D' and resid 62 through 78 Processing helix chain 'D' and resid 83 through 94 Processing helix chain 'D' and resid 96 through 101 removed outlier: 3.618A pdb=" N GLY D 101 " --> pdb=" O LEU D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 113 removed outlier: 3.691A pdb=" N THR D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 148 Processing helix chain 'D' and resid 153 through 173 Processing helix chain 'D' and resid 181 through 199 removed outlier: 4.168A pdb=" N VAL D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 218 Processing helix chain 'D' and resid 236 through 251 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 280 through 287 Processing helix chain 'D' and resid 290 through 308 Processing helix chain 'D' and resid 319 through 335 Processing helix chain 'D' and resid 344 through 348 Processing helix chain 'D' and resid 356 through 376 Processing helix chain 'D' and resid 387 through 392 Processing helix chain 'D' and resid 406 through 412 Processing helix chain 'D' and resid 420 through 425 removed outlier: 3.599A pdb=" N TYR D 424 " --> pdb=" O ARG D 420 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 44 Processing helix chain 'E' and resid 47 through 55 Processing helix chain 'E' and resid 56 through 60 Processing helix chain 'E' and resid 62 through 78 Processing helix chain 'E' and resid 83 through 94 Processing helix chain 'E' and resid 96 through 101 removed outlier: 3.674A pdb=" N GLY E 101 " --> pdb=" O LEU E 97 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 113 removed outlier: 3.713A pdb=" N THR E 113 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 148 Processing helix chain 'E' and resid 153 through 173 Processing helix chain 'E' and resid 174 through 176 No H-bonds generated for 'chain 'E' and resid 174 through 176' Processing helix chain 'E' and resid 182 through 199 Processing helix chain 'E' and resid 213 through 218 Processing helix chain 'E' and resid 236 through 251 Processing helix chain 'E' and resid 264 through 278 Processing helix chain 'E' and resid 280 through 287 Processing helix chain 'E' and resid 290 through 308 Processing helix chain 'E' and resid 319 through 334 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 356 through 376 Processing helix chain 'E' and resid 387 through 392 Processing helix chain 'E' and resid 407 through 412 Processing helix chain 'E' and resid 420 through 425 removed outlier: 3.759A pdb=" N TYR E 424 " --> pdb=" O ARG E 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 44 Processing helix chain 'F' and resid 47 through 55 removed outlier: 3.512A pdb=" N VAL F 51 " --> pdb=" O ARG F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 62 through 78 Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'F' and resid 96 through 101 removed outlier: 3.565A pdb=" N GLY F 101 " --> pdb=" O LEU F 97 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 113 removed outlier: 3.752A pdb=" N THR F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 148 Processing helix chain 'F' and resid 153 through 172 removed outlier: 3.822A pdb=" N ARG F 172 " --> pdb=" O ILE F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 198 removed outlier: 3.888A pdb=" N GLN F 198 " --> pdb=" O GLU F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 218 removed outlier: 3.665A pdb=" N LYS F 217 " --> pdb=" O ASP F 213 " (cutoff:3.500A) Processing helix chain 'F' and resid 236 through 251 Processing helix chain 'F' and resid 264 through 278 Processing helix chain 'F' and resid 280 through 287 Processing helix chain 'F' and resid 290 through 308 Processing helix chain 'F' and resid 319 through 335 Processing helix chain 'F' and resid 344 through 348 Processing helix chain 'F' and resid 356 through 376 Processing helix chain 'F' and resid 387 through 392 removed outlier: 3.626A pdb=" N GLN F 391 " --> pdb=" O ARG F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 406 through 412 Processing helix chain 'F' and resid 420 through 425 removed outlier: 3.657A pdb=" N TYR F 424 " --> pdb=" O ARG F 420 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 180 through 181 removed outlier: 6.778A pdb=" N LEU B 257 " --> pdb=" O MET B 341 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ILE B 340 " --> pdb=" O VAL B 380 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LEU B 382 " --> pdb=" O ILE B 340 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE B 342 " --> pdb=" O LEU B 382 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 229 " --> pdb=" O ALA B 381 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N SER B 383 " --> pdb=" O VAL B 229 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LEU B 226 " --> pdb=" O LEU B 414 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N MET B 416 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N ILE B 228 " --> pdb=" O MET B 416 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE B 418 " --> pdb=" O ILE B 228 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ALA B 230 " --> pdb=" O ILE B 418 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N ILE B 415 " --> pdb=" O GLY B 439 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 310 through 312 removed outlier: 6.323A pdb=" N VAL A 256 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU A 257 " --> pdb=" O MET A 341 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ILE A 340 " --> pdb=" O PRO A 378 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL A 380 " --> pdb=" O ILE A 340 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ILE A 415 " --> pdb=" O GLY A 439 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AA4, first strand: chain 'C' and resid 180 through 181 removed outlier: 3.674A pdb=" N VAL D 229 " --> pdb=" O ALA D 381 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N SER D 383 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N LEU D 226 " --> pdb=" O LEU D 414 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N MET D 416 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ILE D 228 " --> pdb=" O MET D 416 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ILE D 418 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N ALA D 230 " --> pdb=" O ILE D 418 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE D 415 " --> pdb=" O GLY D 439 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 312 through 313 removed outlier: 8.197A pdb=" N ASP C 313 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE C 258 " --> pdb=" O ASP C 313 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU C 257 " --> pdb=" O MET C 341 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU C 382 " --> pdb=" O ILE C 342 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL C 229 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER C 383 " --> pdb=" O VAL C 229 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU C 226 " --> pdb=" O LEU C 414 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N MET C 416 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ILE C 228 " --> pdb=" O MET C 416 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE C 418 " --> pdb=" O ILE C 228 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ALA C 230 " --> pdb=" O ILE C 418 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE C 415 " --> pdb=" O GLY C 439 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 180 through 181 removed outlier: 6.774A pdb=" N LEU F 257 " --> pdb=" O MET F 341 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE F 340 " --> pdb=" O VAL F 380 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU F 382 " --> pdb=" O ILE F 340 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N ILE F 342 " --> pdb=" O LEU F 382 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL F 229 " --> pdb=" O ALA F 381 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU F 226 " --> pdb=" O LEU F 414 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N MET F 416 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE F 228 " --> pdb=" O MET F 416 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE F 418 " --> pdb=" O ILE F 228 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N ALA F 230 " --> pdb=" O ILE F 418 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE F 415 " --> pdb=" O GLY F 439 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 310 through 313 removed outlier: 6.751A pdb=" N VAL E 256 " --> pdb=" O TYR E 311 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N ASP E 313 " --> pdb=" O VAL E 256 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE E 258 " --> pdb=" O ASP E 313 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU E 257 " --> pdb=" O MET E 341 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL E 229 " --> pdb=" O ALA E 381 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER E 383 " --> pdb=" O VAL E 229 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU E 226 " --> pdb=" O LEU E 414 " (cutoff:3.500A) removed outlier: 7.239A pdb=" N MET E 416 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE E 228 " --> pdb=" O MET E 416 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ILE E 418 " --> pdb=" O ILE E 228 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ALA E 230 " --> pdb=" O ILE E 418 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE E 415 " --> pdb=" O GLY E 439 " (cutoff:3.500A) 1226 hydrogen bonds defined for protein. 3570 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: 4.01 Time building geometry restraints manager: 1.77 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: 6851 1.34 - 1.45: 2267 1.45 - 1.57: 12106 1.57 - 1.69: 40 1.69 - 1.81: 159 Bond restraints: 21423 Sorted by residual: bond pdb=" O3A ANP E1001 " pdb=" PB ANP E1001 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" O3A ANP C1001 " pdb=" PB ANP C1001 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.43e+01 bond pdb=" O3A ANP D1001 " pdb=" PB ANP D1001 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.32e+01 bond pdb=" O3A ANP F1001 " pdb=" PB ANP F1001 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.24e+01 bond pdb=" N3B ANP E1001 " pdb=" PG ANP E1001 " ideal model delta sigma weight residual 1.795 1.687 0.108 2.00e-02 2.50e+03 2.94e+01 ... (remaining 21418 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.90: 28959 3.90 - 7.79: 63 7.79 - 11.69: 9 11.69 - 15.59: 2 15.59 - 19.48: 2 Bond angle restraints: 29035 Sorted by residual: angle pdb=" PB ANP E1001 " pdb=" N3B ANP E1001 " pdb=" PG ANP E1001 " ideal model delta sigma weight residual 126.95 107.47 19.48 3.00e+00 1.11e-01 4.22e+01 angle pdb=" PB ANP C1001 " pdb=" N3B ANP C1001 " pdb=" PG ANP C1001 " ideal model delta sigma weight residual 126.95 109.26 17.69 3.00e+00 1.11e-01 3.48e+01 angle pdb=" PB ANP D1001 " pdb=" N3B ANP D1001 " pdb=" PG ANP D1001 " ideal model delta sigma weight residual 126.95 111.63 15.32 3.00e+00 1.11e-01 2.61e+01 angle pdb=" PB ANP F1001 " pdb=" N3B ANP F1001 " pdb=" PG ANP F1001 " ideal model delta sigma weight residual 126.95 111.98 14.97 3.00e+00 1.11e-01 2.49e+01 angle pdb=" C SER D 234 " pdb=" CA SER D 234 " pdb=" CB SER D 234 " ideal model delta sigma weight residual 117.23 111.21 6.02 1.36e+00 5.41e-01 1.96e+01 ... (remaining 29030 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.79: 13005 31.79 - 63.58: 245 63.58 - 95.38: 42 95.38 - 127.17: 0 127.17 - 158.96: 1 Dihedral angle restraints: 13293 sinusoidal: 5589 harmonic: 7704 Sorted by residual: dihedral pdb=" CA TYR E 344 " pdb=" C TYR E 344 " pdb=" N LEU E 345 " pdb=" CA LEU E 345 " ideal model delta harmonic sigma weight residual -180.00 -156.90 -23.10 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" O1A ANP C1001 " pdb=" O3A ANP C1001 " pdb=" PA ANP C1001 " pdb=" PB ANP C1001 " ideal model delta sinusoidal sigma weight residual 83.11 -75.85 158.96 1 3.00e+01 1.11e-03 2.06e+01 dihedral pdb=" CA TYR B 344 " pdb=" C TYR B 344 " pdb=" N LEU B 345 " pdb=" CA LEU B 345 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 13290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2788 0.055 - 0.110: 468 0.110 - 0.165: 30 0.165 - 0.220: 0 0.220 - 0.275: 4 Chirality restraints: 3290 Sorted by residual: chirality pdb=" C3' ANP E1001 " pdb=" C2' ANP E1001 " pdb=" C4' ANP E1001 " pdb=" O3' ANP E1001 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' ANP C1001 " pdb=" C2' ANP C1001 " pdb=" C4' ANP C1001 " pdb=" O3' ANP C1001 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' ANP F1001 " pdb=" C2' ANP F1001 " pdb=" C4' ANP F1001 " pdb=" O3' ANP F1001 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 3287 not shown) Planarity restraints: 3812 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 232 " 0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO D 233 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO D 233 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 233 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 63 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO B 64 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO B 64 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 64 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 63 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO E 64 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO E 64 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 64 " -0.021 5.00e-02 4.00e+02 ... (remaining 3809 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 377 2.64 - 3.21: 19205 3.21 - 3.77: 36407 3.77 - 4.34: 48534 4.34 - 4.90: 77351 Nonbonded interactions: 181874 Sorted by model distance: nonbonded pdb=" OG1 THR D 238 " pdb="MG MG D1002 " model vdw 2.079 2.170 nonbonded pdb=" OG1 THR E 238 " pdb="MG MG E1002 " model vdw 2.079 2.170 nonbonded pdb=" O2G ANP C1001 " pdb="MG MG C1002 " model vdw 2.079 2.170 nonbonded pdb=" O2B ANP D1001 " pdb="MG MG D1002 " model vdw 2.079 2.170 nonbonded pdb=" O2G ANP E1001 " pdb="MG MG E1002 " model vdw 2.079 2.170 ... (remaining 181869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 25 through 464) selection = (chain 'C' and resid 25 through 464) selection = (chain 'D' and resid 25 through 464) selection = (chain 'E' and resid 25 through 464) selection = (chain 'F' and resid 25 through 464) } 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: 1.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 18.820 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.040 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 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 : 0.004 0.148 21423 Z= 0.204 Angle : 0.635 19.484 29035 Z= 0.350 Chirality : 0.039 0.275 3290 Planarity : 0.004 0.052 3812 Dihedral : 12.589 158.959 8301 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.27 % Favored : 97.58 % Rotamer: Outliers : 3.24 % Allowed : 4.88 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.16), residues: 2649 helix: 1.78 (0.13), residues: 1473 sheet: -2.17 (0.25), residues: 314 loop : -0.79 (0.21), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 66 TYR 0.023 0.001 TYR F 344 PHE 0.010 0.001 PHE D 166 TRP 0.010 0.001 TRP A 457 HIS 0.002 0.001 HIS D 334 Details of bonding type rmsd covalent geometry : bond 0.00385 (21423) covalent geometry : angle 0.63482 (29035) hydrogen bonds : bond 0.13716 ( 1226) hydrogen bonds : angle 5.27944 ( 3570) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 403 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 268 ILE cc_start: 0.9283 (mm) cc_final: 0.9003 (pt) REVERT: A 339 LEU cc_start: 0.8704 (tp) cc_final: 0.8473 (mp) REVERT: A 347 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8305 (mm) REVERT: B 50 ASP cc_start: 0.9457 (OUTLIER) cc_final: 0.9159 (p0) REVERT: B 235 MET cc_start: 0.4420 (mmt) cc_final: 0.3816 (mmm) REVERT: B 268 ILE cc_start: 0.9261 (mm) cc_final: 0.9029 (pt) REVERT: B 345 LEU cc_start: 0.9479 (mt) cc_final: 0.9258 (mt) REVERT: C 212 ASP cc_start: 0.9566 (OUTLIER) cc_final: 0.9215 (p0) REVERT: C 371 LEU cc_start: 0.9607 (tp) cc_final: 0.9306 (tp) REVERT: D 235 MET cc_start: 0.7917 (mmt) cc_final: 0.7340 (mmm) REVERT: D 240 PHE cc_start: 0.9386 (t80) cc_final: 0.9102 (t80) REVERT: D 263 MET cc_start: 0.8874 (mtp) cc_final: 0.8663 (mtt) REVERT: D 382 LEU cc_start: 0.9143 (mt) cc_final: 0.8885 (mt) REVERT: D 411 ASP cc_start: 0.7797 (m-30) cc_final: 0.7343 (t0) REVERT: E 49 ASP cc_start: 0.9578 (OUTLIER) cc_final: 0.9367 (p0) REVERT: E 315 SER cc_start: 0.8694 (m) cc_final: 0.8336 (p) REVERT: E 390 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8703 (mp0) REVERT: F 105 TYR cc_start: 0.9314 (t80) cc_final: 0.9094 (t80) REVERT: F 159 ASP cc_start: 0.9401 (m-30) cc_final: 0.9016 (p0) REVERT: F 263 MET cc_start: 0.8659 (mtt) cc_final: 0.8141 (mtt) REVERT: F 382 LEU cc_start: 0.8597 (mt) cc_final: 0.7882 (mp) REVERT: F 389 LEU cc_start: 0.9198 (tt) cc_final: 0.8948 (tt) outliers start: 73 outliers final: 15 residues processed: 471 average time/residue: 0.1631 time to fit residues: 114.5096 Evaluate side-chains 265 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 246 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 50.0000 chunk 132 optimal weight: 0.0670 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 4.9990 overall best weight: 5.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 425 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 96 GLN C 252 GLN C 454 ASN D 65 HIS D 252 GLN D 281 GLN D 454 ASN E 199 GLN ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 ASN ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN F 467 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.040750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.025313 restraints weight = 196446.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.026325 restraints weight = 145777.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.027144 restraints weight = 116133.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.027806 restraints weight = 97052.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.028260 restraints weight = 83921.231| |-----------------------------------------------------------------------------| r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 21423 Z= 0.182 Angle : 0.605 9.160 29035 Z= 0.316 Chirality : 0.040 0.192 3290 Planarity : 0.005 0.072 3812 Dihedral : 9.525 166.347 3150 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.06 % Favored : 96.83 % Rotamer: Outliers : 0.35 % Allowed : 2.13 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.17), residues: 2649 helix: 2.04 (0.13), residues: 1506 sheet: -1.84 (0.26), residues: 319 loop : -0.42 (0.23), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 63 TYR 0.020 0.002 TYR B 344 PHE 0.027 0.002 PHE A 460 TRP 0.025 0.002 TRP B 457 HIS 0.011 0.002 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00387 (21423) covalent geometry : angle 0.60497 (29035) hydrogen bonds : bond 0.03667 ( 1226) hydrogen bonds : angle 4.45637 ( 3570) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 294 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.9681 (tpt) cc_final: 0.9406 (tpp) REVERT: A 341 MET cc_start: 0.8218 (ttt) cc_final: 0.6140 (ppp) REVERT: B 172 ARG cc_start: 0.7100 (tpt170) cc_final: 0.6839 (tpt170) REVERT: B 347 LEU cc_start: 0.9331 (mm) cc_final: 0.8846 (tt) REVERT: B 348 MET cc_start: 0.9614 (mmm) cc_final: 0.8985 (tpt) REVERT: D 281 GLN cc_start: 0.9202 (OUTLIER) cc_final: 0.8742 (pp30) REVERT: E 242 MET cc_start: 0.8455 (ttp) cc_final: 0.8175 (ptm) REVERT: F 106 LEU cc_start: 0.9877 (mt) cc_final: 0.9523 (mt) REVERT: F 240 PHE cc_start: 0.9855 (t80) cc_final: 0.9545 (t80) REVERT: F 242 MET cc_start: 0.8694 (ttp) cc_final: 0.8164 (ptm) outliers start: 8 outliers final: 3 residues processed: 301 average time/residue: 0.1714 time to fit residues: 76.2863 Evaluate side-chains 209 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 205 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 216 optimal weight: 9.9990 chunk 247 optimal weight: 8.9990 chunk 167 optimal weight: 4.9990 chunk 244 optimal weight: 5.9990 chunk 255 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 188 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 252 GLN D 281 GLN ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.067226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.053039 restraints weight = 229667.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.054597 restraints weight = 120172.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.054882 restraints weight = 71369.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.055180 restraints weight = 67845.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.055364 restraints weight = 56377.429| |-----------------------------------------------------------------------------| r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21423 Z= 0.145 Angle : 0.556 9.030 29035 Z= 0.288 Chirality : 0.040 0.190 3290 Planarity : 0.004 0.047 3812 Dihedral : 8.318 150.622 3150 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.83 % Rotamer: Outliers : 0.13 % Allowed : 2.22 % Favored : 97.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.17), residues: 2649 helix: 1.85 (0.13), residues: 1515 sheet: -1.57 (0.27), residues: 306 loop : -0.40 (0.23), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 366 TYR 0.021 0.001 TYR A 344 PHE 0.027 0.002 PHE C 259 TRP 0.018 0.001 TRP A 48 HIS 0.005 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00303 (21423) covalent geometry : angle 0.55639 (29035) hydrogen bonds : bond 0.03328 ( 1226) hydrogen bonds : angle 4.28124 ( 3570) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 277 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.9764 (tpt) cc_final: 0.9394 (tpp) REVERT: A 341 MET cc_start: 0.7888 (ttt) cc_final: 0.6089 (ppp) REVERT: B 235 MET cc_start: 0.4262 (mmm) cc_final: 0.3922 (mmm) REVERT: B 347 LEU cc_start: 0.9295 (mm) cc_final: 0.8874 (tt) REVERT: B 348 MET cc_start: 0.9595 (mmm) cc_final: 0.9228 (tpt) REVERT: C 415 ILE cc_start: 0.9853 (mt) cc_final: 0.9526 (mp) REVERT: D 105 TYR cc_start: 0.8824 (t80) cc_final: 0.8447 (t80) REVERT: D 226 LEU cc_start: 0.9663 (tp) cc_final: 0.9458 (tp) REVERT: D 281 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8394 (pp30) REVERT: D 348 MET cc_start: 0.9725 (mmm) cc_final: 0.9311 (tpt) REVERT: D 410 GLN cc_start: 0.9444 (mt0) cc_final: 0.9186 (mm-40) REVERT: E 142 ILE cc_start: 0.9740 (mm) cc_final: 0.9363 (mm) REVERT: E 263 MET cc_start: 0.8967 (mmp) cc_final: 0.8565 (mmm) REVERT: F 105 TYR cc_start: 0.8991 (t80) cc_final: 0.8655 (t80) REVERT: F 242 MET cc_start: 0.8576 (ttp) cc_final: 0.8268 (ptm) REVERT: F 270 MET cc_start: 0.9578 (ttt) cc_final: 0.8762 (tmm) REVERT: F 418 ILE cc_start: 0.9598 (mp) cc_final: 0.9219 (mp) outliers start: 3 outliers final: 1 residues processed: 280 average time/residue: 0.1687 time to fit residues: 69.6309 Evaluate side-chains 206 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 204 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 95 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 chunk 264 optimal weight: 40.0000 chunk 229 optimal weight: 0.8980 chunk 51 optimal weight: 6.9990 chunk 145 optimal weight: 7.9990 chunk 192 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 203 optimal weight: 3.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 140 ASN D 281 GLN E 140 ASN ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 GLN E 454 ASN F 281 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.064434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.050732 restraints weight = 235453.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.051737 restraints weight = 131271.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.052365 restraints weight = 82824.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.052613 restraints weight = 73225.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.052732 restraints weight = 60967.324| |-----------------------------------------------------------------------------| r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 21423 Z= 0.160 Angle : 0.581 9.687 29035 Z= 0.304 Chirality : 0.040 0.253 3290 Planarity : 0.005 0.114 3812 Dihedral : 7.398 143.325 3150 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.32 % Favored : 96.60 % Rotamer: Outliers : 0.09 % Allowed : 2.22 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.17), residues: 2649 helix: 1.71 (0.13), residues: 1515 sheet: -1.36 (0.27), residues: 318 loop : -0.43 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 152 TYR 0.014 0.002 TYR A 344 PHE 0.024 0.002 PHE C 259 TRP 0.017 0.001 TRP A 457 HIS 0.005 0.001 HIS E 29 Details of bonding type rmsd covalent geometry : bond 0.00333 (21423) covalent geometry : angle 0.58106 (29035) hydrogen bonds : bond 0.03230 ( 1226) hydrogen bonds : angle 4.37451 ( 3570) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 252 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.9793 (tpt) cc_final: 0.9404 (tpp) REVERT: A 341 MET cc_start: 0.7873 (ttt) cc_final: 0.6081 (ppp) REVERT: B 235 MET cc_start: 0.4946 (mmm) cc_final: 0.4511 (mmm) REVERT: B 348 MET cc_start: 0.9547 (mmm) cc_final: 0.9138 (tpt) REVERT: C 242 MET cc_start: 0.9698 (tpt) cc_final: 0.9479 (tpp) REVERT: D 105 TYR cc_start: 0.8901 (t80) cc_final: 0.8548 (t80) REVERT: D 240 PHE cc_start: 0.9756 (t80) cc_final: 0.9535 (t80) REVERT: D 281 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8419 (pp30) REVERT: D 410 GLN cc_start: 0.9583 (mt0) cc_final: 0.9212 (mm-40) REVERT: D 416 MET cc_start: 0.9372 (mmm) cc_final: 0.9128 (mmm) REVERT: D 417 PHE cc_start: 0.9413 (m-80) cc_final: 0.9115 (m-80) REVERT: E 348 MET cc_start: 0.9581 (tpt) cc_final: 0.9048 (tpt) REVERT: E 417 PHE cc_start: 0.9234 (m-80) cc_final: 0.9007 (m-80) REVERT: F 105 TYR cc_start: 0.9130 (t80) cc_final: 0.8803 (t80) REVERT: F 242 MET cc_start: 0.8538 (ttp) cc_final: 0.8255 (ptm) REVERT: F 418 ILE cc_start: 0.9647 (mp) cc_final: 0.9302 (mp) outliers start: 2 outliers final: 1 residues processed: 254 average time/residue: 0.1669 time to fit residues: 63.6605 Evaluate side-chains 190 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 18 optimal weight: 50.0000 chunk 117 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 64 optimal weight: 30.0000 chunk 202 optimal weight: 5.9990 chunk 209 optimal weight: 5.9990 chunk 174 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 160 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN B 443 ASN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN E 243 ASN E 247 ASN F 252 GLN ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.062999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.049521 restraints weight = 236770.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.050468 restraints weight = 131686.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.050912 restraints weight = 84557.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.051225 restraints weight = 75010.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.051407 restraints weight = 62164.398| |-----------------------------------------------------------------------------| r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 21423 Z= 0.161 Angle : 0.580 10.823 29035 Z= 0.303 Chirality : 0.041 0.238 3290 Planarity : 0.004 0.052 3812 Dihedral : 6.929 141.000 3150 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.44 % Favored : 96.53 % Rotamer: Outliers : 0.27 % Allowed : 1.77 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.17), residues: 2649 helix: 1.64 (0.13), residues: 1514 sheet: -1.15 (0.28), residues: 318 loop : -0.44 (0.23), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 442 TYR 0.013 0.002 TYR B 344 PHE 0.017 0.002 PHE A 259 TRP 0.020 0.001 TRP A 457 HIS 0.005 0.001 HIS A 67 Details of bonding type rmsd covalent geometry : bond 0.00334 (21423) covalent geometry : angle 0.58041 (29035) hydrogen bonds : bond 0.03201 ( 1226) hydrogen bonds : angle 4.37738 ( 3570) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 243 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.9802 (tpt) cc_final: 0.9418 (tpp) REVERT: A 339 LEU cc_start: 0.9546 (mm) cc_final: 0.9076 (pp) REVERT: A 341 MET cc_start: 0.7617 (ttt) cc_final: 0.5851 (ppp) REVERT: B 235 MET cc_start: 0.5455 (mmm) cc_final: 0.5099 (mmm) REVERT: B 270 MET cc_start: 0.9505 (mtm) cc_final: 0.9224 (tmm) REVERT: B 348 MET cc_start: 0.9500 (mmm) cc_final: 0.9293 (mmm) REVERT: C 242 MET cc_start: 0.9669 (tpt) cc_final: 0.9459 (tpp) REVERT: D 105 TYR cc_start: 0.8949 (t80) cc_final: 0.8582 (t80) REVERT: D 281 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8436 (pp30) REVERT: D 348 MET cc_start: 0.9725 (mmm) cc_final: 0.9425 (tpp) REVERT: D 410 GLN cc_start: 0.9537 (mt0) cc_final: 0.9327 (mm110) REVERT: D 417 PHE cc_start: 0.9464 (m-80) cc_final: 0.9179 (m-80) REVERT: E 348 MET cc_start: 0.9679 (tpt) cc_final: 0.9222 (tpt) REVERT: E 417 PHE cc_start: 0.9283 (m-80) cc_final: 0.9026 (m-80) REVERT: F 105 TYR cc_start: 0.9239 (t80) cc_final: 0.8911 (t80) REVERT: F 240 PHE cc_start: 0.9837 (t80) cc_final: 0.9633 (t80) REVERT: F 242 MET cc_start: 0.8611 (ttp) cc_final: 0.8318 (ptm) REVERT: F 270 MET cc_start: 0.9587 (ttt) cc_final: 0.8730 (tmm) outliers start: 6 outliers final: 2 residues processed: 249 average time/residue: 0.1632 time to fit residues: 61.8596 Evaluate side-chains 184 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 181 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 57 optimal weight: 6.9990 chunk 178 optimal weight: 6.9990 chunk 75 optimal weight: 40.0000 chunk 234 optimal weight: 7.9990 chunk 138 optimal weight: 5.9990 chunk 187 optimal weight: 5.9990 chunk 218 optimal weight: 20.0000 chunk 108 optimal weight: 5.9990 chunk 251 optimal weight: 20.0000 chunk 232 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 112 ASN ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN E 454 ASN ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.062157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.048731 restraints weight = 239660.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.049791 restraints weight = 128512.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.050176 restraints weight = 83481.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.050486 restraints weight = 77352.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.050891 restraints weight = 62675.065| |-----------------------------------------------------------------------------| r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21423 Z= 0.161 Angle : 0.587 10.402 29035 Z= 0.306 Chirality : 0.041 0.228 3290 Planarity : 0.004 0.042 3812 Dihedral : 6.684 140.350 3150 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.66 % Favored : 96.30 % Rotamer: Outliers : 0.04 % Allowed : 1.15 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.17), residues: 2649 helix: 1.52 (0.13), residues: 1524 sheet: -1.06 (0.29), residues: 309 loop : -0.51 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 63 TYR 0.015 0.002 TYR A 344 PHE 0.025 0.002 PHE A 147 TRP 0.015 0.001 TRP A 457 HIS 0.004 0.001 HIS E 29 Details of bonding type rmsd covalent geometry : bond 0.00327 (21423) covalent geometry : angle 0.58674 (29035) hydrogen bonds : bond 0.03209 ( 1226) hydrogen bonds : angle 4.45856 ( 3570) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 PHE cc_start: 0.9535 (t80) cc_final: 0.9318 (t80) REVERT: A 242 MET cc_start: 0.9794 (tpt) cc_final: 0.9420 (tpp) REVERT: A 339 LEU cc_start: 0.9555 (mm) cc_final: 0.9128 (pp) REVERT: A 341 MET cc_start: 0.7599 (ttt) cc_final: 0.5745 (ppp) REVERT: B 235 MET cc_start: 0.5000 (mmm) cc_final: 0.4658 (mmm) REVERT: B 348 MET cc_start: 0.9504 (mmm) cc_final: 0.9128 (tpt) REVERT: C 263 MET cc_start: 0.8849 (mmt) cc_final: 0.8647 (mmt) REVERT: C 348 MET cc_start: 0.9399 (mmp) cc_final: 0.8877 (tpp) REVERT: D 105 TYR cc_start: 0.8904 (t80) cc_final: 0.8566 (t80) REVERT: D 281 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8375 (pp30) REVERT: D 348 MET cc_start: 0.9750 (mmm) cc_final: 0.9492 (tpp) REVERT: D 410 GLN cc_start: 0.9561 (mt0) cc_final: 0.9331 (mm110) REVERT: D 417 PHE cc_start: 0.9454 (m-80) cc_final: 0.9184 (m-80) REVERT: E 301 MET cc_start: 0.9748 (ptp) cc_final: 0.9516 (ptp) REVERT: E 348 MET cc_start: 0.9672 (tpt) cc_final: 0.9365 (tpt) REVERT: E 417 PHE cc_start: 0.9234 (m-80) cc_final: 0.8922 (m-80) REVERT: F 105 TYR cc_start: 0.9220 (t80) cc_final: 0.8913 (t80) REVERT: F 242 MET cc_start: 0.8518 (ttp) cc_final: 0.8255 (ptm) REVERT: F 270 MET cc_start: 0.9547 (ttt) cc_final: 0.8724 (tmm) outliers start: 1 outliers final: 0 residues processed: 238 average time/residue: 0.1545 time to fit residues: 56.1968 Evaluate side-chains 178 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 25 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 241 optimal weight: 8.9990 chunk 161 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 234 optimal weight: 0.5980 chunk 227 optimal weight: 30.0000 chunk 132 optimal weight: 4.9990 chunk 61 optimal weight: 30.0000 chunk 117 optimal weight: 0.8980 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.037746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2550 r_free = 0.2550 target = 0.025040 restraints weight = 236533.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.025767 restraints weight = 188397.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.026337 restraints weight = 158047.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.026802 restraints weight = 137832.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.027166 restraints weight = 123598.567| |-----------------------------------------------------------------------------| r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21423 Z= 0.143 Angle : 0.561 10.050 29035 Z= 0.292 Chirality : 0.040 0.190 3290 Planarity : 0.004 0.042 3812 Dihedral : 6.580 139.899 3150 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.59 % Favored : 96.38 % Rotamer: Outliers : 0.04 % Allowed : 1.06 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.17), residues: 2649 helix: 1.55 (0.13), residues: 1524 sheet: -0.85 (0.29), residues: 320 loop : -0.42 (0.24), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 74 TYR 0.013 0.001 TYR B 105 PHE 0.025 0.002 PHE E 166 TRP 0.014 0.001 TRP A 457 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00296 (21423) covalent geometry : angle 0.56135 (29035) hydrogen bonds : bond 0.03071 ( 1226) hydrogen bonds : angle 4.38184 ( 3570) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.9384 (m-10) cc_final: 0.9068 (m-80) REVERT: A 69 PHE cc_start: 0.9647 (t80) cc_final: 0.9284 (t80) REVERT: A 164 ARG cc_start: 0.9693 (mpt180) cc_final: 0.9351 (mtt-85) REVERT: A 242 MET cc_start: 0.9845 (tpt) cc_final: 0.9442 (tpp) REVERT: A 339 LEU cc_start: 0.9482 (mm) cc_final: 0.9205 (pp) REVERT: A 341 MET cc_start: 0.7471 (ttt) cc_final: 0.5735 (ppp) REVERT: B 235 MET cc_start: 0.6181 (mmm) cc_final: 0.5872 (mmm) REVERT: B 348 MET cc_start: 0.9608 (mmm) cc_final: 0.9288 (tpt) REVERT: C 242 MET cc_start: 0.9587 (tpt) cc_final: 0.9352 (tpp) REVERT: C 263 MET cc_start: 0.9013 (mmt) cc_final: 0.8361 (mmt) REVERT: C 348 MET cc_start: 0.9348 (mmp) cc_final: 0.8773 (tpt) REVERT: C 442 ARG cc_start: 0.8277 (ttm110) cc_final: 0.8010 (ttm-80) REVERT: D 105 TYR cc_start: 0.9200 (t80) cc_final: 0.8994 (t80) REVERT: D 240 PHE cc_start: 0.9747 (t80) cc_final: 0.9468 (t80) REVERT: D 281 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8943 (pp30) REVERT: D 348 MET cc_start: 0.9685 (mmm) cc_final: 0.9477 (tpp) REVERT: D 416 MET cc_start: 0.9323 (mmm) cc_final: 0.8972 (mmm) REVERT: D 417 PHE cc_start: 0.9339 (m-80) cc_final: 0.9027 (m-80) REVERT: E 263 MET cc_start: 0.9037 (mmm) cc_final: 0.8815 (mmm) REVERT: E 301 MET cc_start: 0.9809 (ptp) cc_final: 0.9573 (ptp) REVERT: E 417 PHE cc_start: 0.9162 (m-80) cc_final: 0.8804 (m-80) REVERT: F 105 TYR cc_start: 0.9487 (t80) cc_final: 0.9167 (t80) REVERT: F 270 MET cc_start: 0.9698 (ttt) cc_final: 0.8680 (tmm) outliers start: 1 outliers final: 0 residues processed: 235 average time/residue: 0.1576 time to fit residues: 56.5460 Evaluate side-chains 177 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 176 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 57 optimal weight: 7.9990 chunk 243 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 225 optimal weight: 7.9990 chunk 116 optimal weight: 0.4980 chunk 111 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 2 optimal weight: 0.2980 chunk 193 optimal weight: 2.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 HIS ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 462 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.063026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.049195 restraints weight = 235343.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.050425 restraints weight = 129765.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.050907 restraints weight = 78982.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.051135 restraints weight = 75430.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.051242 restraints weight = 62584.646| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 21423 Z= 0.121 Angle : 0.558 10.627 29035 Z= 0.290 Chirality : 0.040 0.189 3290 Planarity : 0.004 0.043 3812 Dihedral : 6.528 139.129 3150 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.17), residues: 2649 helix: 1.60 (0.13), residues: 1518 sheet: -0.78 (0.29), residues: 317 loop : -0.46 (0.24), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 164 TYR 0.013 0.001 TYR B 105 PHE 0.032 0.002 PHE B 240 TRP 0.012 0.001 TRP B 48 HIS 0.008 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00257 (21423) covalent geometry : angle 0.55797 (29035) hydrogen bonds : bond 0.03043 ( 1226) hydrogen bonds : angle 4.35163 ( 3570) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 PHE cc_start: 0.9478 (t80) cc_final: 0.9247 (t80) REVERT: A 242 MET cc_start: 0.9786 (tpt) cc_final: 0.9404 (tpp) REVERT: A 339 LEU cc_start: 0.9541 (mm) cc_final: 0.9218 (pp) REVERT: A 341 MET cc_start: 0.7611 (ttt) cc_final: 0.5790 (ppp) REVERT: B 270 MET cc_start: 0.9508 (mtm) cc_final: 0.9183 (mmm) REVERT: B 348 MET cc_start: 0.9348 (mmm) cc_final: 0.8997 (tpt) REVERT: C 242 MET cc_start: 0.9598 (tpt) cc_final: 0.9371 (tpp) REVERT: C 348 MET cc_start: 0.9347 (mmp) cc_final: 0.8762 (tpt) REVERT: D 417 PHE cc_start: 0.9382 (m-80) cc_final: 0.9127 (m-80) REVERT: E 301 MET cc_start: 0.9654 (ptp) cc_final: 0.9400 (ptp) REVERT: E 348 MET cc_start: 0.9548 (tpt) cc_final: 0.9185 (tpt) REVERT: E 417 PHE cc_start: 0.9166 (m-80) cc_final: 0.8886 (m-80) REVERT: F 105 TYR cc_start: 0.9158 (t80) cc_final: 0.8894 (t80) REVERT: F 106 LEU cc_start: 0.9786 (mt) cc_final: 0.9475 (mt) REVERT: F 270 MET cc_start: 0.9483 (ttt) cc_final: 0.8731 (tmm) REVERT: F 348 MET cc_start: 0.9891 (mpp) cc_final: 0.9646 (mpp) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1613 time to fit residues: 56.5712 Evaluate side-chains 176 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 126 optimal weight: 9.9990 chunk 244 optimal weight: 5.9990 chunk 130 optimal weight: 0.6980 chunk 202 optimal weight: 8.9990 chunk 89 optimal weight: 20.0000 chunk 42 optimal weight: 40.0000 chunk 138 optimal weight: 20.0000 chunk 146 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.061791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.048354 restraints weight = 237797.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.049277 restraints weight = 133012.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.049767 restraints weight = 83403.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.050087 restraints weight = 74542.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.050348 restraints weight = 61372.105| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21423 Z= 0.138 Angle : 0.573 12.705 29035 Z= 0.298 Chirality : 0.040 0.184 3290 Planarity : 0.004 0.093 3812 Dihedral : 6.637 136.379 3150 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.17), residues: 2649 helix: 1.60 (0.13), residues: 1519 sheet: -0.82 (0.29), residues: 317 loop : -0.46 (0.24), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 164 TYR 0.013 0.001 TYR E 311 PHE 0.019 0.002 PHE B 240 TRP 0.013 0.001 TRP B 48 HIS 0.006 0.001 HIS D 65 Details of bonding type rmsd covalent geometry : bond 0.00289 (21423) covalent geometry : angle 0.57330 (29035) hydrogen bonds : bond 0.03077 ( 1226) hydrogen bonds : angle 4.39048 ( 3570) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 242 MET cc_start: 0.9769 (tpt) cc_final: 0.9411 (tpp) REVERT: A 339 LEU cc_start: 0.9503 (mm) cc_final: 0.9234 (pp) REVERT: A 341 MET cc_start: 0.7682 (ttt) cc_final: 0.5853 (ppp) REVERT: C 164 ARG cc_start: 0.9628 (mpt180) cc_final: 0.9409 (mmt-90) REVERT: C 345 LEU cc_start: 0.9888 (pp) cc_final: 0.9683 (pp) REVERT: C 348 MET cc_start: 0.9346 (mmp) cc_final: 0.8598 (tpp) REVERT: D 172 ARG cc_start: 0.9042 (mmt180) cc_final: 0.8783 (ptt180) REVERT: D 348 MET cc_start: 0.9752 (tpt) cc_final: 0.9479 (tpt) REVERT: E 242 MET cc_start: 0.7812 (tmm) cc_final: 0.7438 (tmm) REVERT: E 257 LEU cc_start: 0.9845 (tp) cc_final: 0.9428 (pp) REVERT: E 301 MET cc_start: 0.9603 (ptp) cc_final: 0.9315 (ptp) REVERT: E 348 MET cc_start: 0.9540 (tpt) cc_final: 0.9265 (tpt) REVERT: E 417 PHE cc_start: 0.9090 (m-80) cc_final: 0.8826 (m-80) REVERT: F 82 ILE cc_start: 0.4930 (mt) cc_final: 0.4584 (mt) REVERT: F 105 TYR cc_start: 0.9083 (t80) cc_final: 0.8844 (t80) REVERT: F 270 MET cc_start: 0.9444 (ttt) cc_final: 0.8896 (tmm) REVERT: F 348 MET cc_start: 0.9882 (mpp) cc_final: 0.9655 (mpp) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1581 time to fit residues: 55.7823 Evaluate side-chains 174 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 255 optimal weight: 30.0000 chunk 256 optimal weight: 10.0000 chunk 246 optimal weight: 0.5980 chunk 1 optimal weight: 8.9990 chunk 212 optimal weight: 8.9990 chunk 240 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 167 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 257 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 410 GLN ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.060148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.046743 restraints weight = 243375.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.048048 restraints weight = 138153.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.048384 restraints weight = 79866.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.048697 restraints weight = 76551.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.048985 restraints weight = 61989.640| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.5132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 21423 Z= 0.166 Angle : 0.607 13.776 29035 Z= 0.317 Chirality : 0.041 0.187 3290 Planarity : 0.004 0.083 3812 Dihedral : 6.751 135.483 3150 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.96 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.17), residues: 2649 helix: 1.47 (0.13), residues: 1528 sheet: -0.83 (0.29), residues: 316 loop : -0.58 (0.24), residues: 805 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 164 TYR 0.014 0.002 TYR D 344 PHE 0.020 0.002 PHE B 240 TRP 0.016 0.001 TRP B 48 HIS 0.004 0.001 HIS E 29 Details of bonding type rmsd covalent geometry : bond 0.00341 (21423) covalent geometry : angle 0.60682 (29035) hydrogen bonds : bond 0.03228 ( 1226) hydrogen bonds : angle 4.47537 ( 3570) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5298 Ramachandran restraints generated. 2649 Oldfield, 0 Emsley, 2649 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 PHE cc_start: 0.9040 (m-80) cc_final: 0.8762 (m-80) REVERT: A 242 MET cc_start: 0.9773 (tpt) cc_final: 0.9405 (tpp) REVERT: A 339 LEU cc_start: 0.9507 (mm) cc_final: 0.9261 (pp) REVERT: A 341 MET cc_start: 0.7640 (ttt) cc_final: 0.5687 (ppp) REVERT: C 345 LEU cc_start: 0.9896 (pp) cc_final: 0.9684 (pp) REVERT: C 348 MET cc_start: 0.9408 (mmp) cc_final: 0.8619 (tpp) REVERT: D 172 ARG cc_start: 0.9107 (mmt180) cc_final: 0.8846 (ptt180) REVERT: D 348 MET cc_start: 0.9732 (tpt) cc_final: 0.9402 (tpt) REVERT: E 257 LEU cc_start: 0.9830 (tp) cc_final: 0.9574 (tp) REVERT: E 270 MET cc_start: 0.9569 (ppp) cc_final: 0.9338 (ppp) REVERT: E 301 MET cc_start: 0.9625 (ptp) cc_final: 0.9339 (ptp) REVERT: E 348 MET cc_start: 0.9590 (tpt) cc_final: 0.9310 (tpt) REVERT: E 417 PHE cc_start: 0.9147 (m-80) cc_final: 0.8852 (m-80) REVERT: F 105 TYR cc_start: 0.9181 (t80) cc_final: 0.8940 (t80) REVERT: F 270 MET cc_start: 0.9432 (ttt) cc_final: 0.8845 (tmm) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.1530 time to fit residues: 51.9412 Evaluate side-chains 169 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 265 random chunks: chunk 82 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 152 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 109 optimal weight: 0.9980 chunk 150 optimal weight: 7.9990 chunk 222 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 110 optimal weight: 6.9990 chunk 158 optimal weight: 20.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 ASN B 222 GLN B 454 ASN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 247 ASN ** C 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.058995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.045934 restraints weight = 246243.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.046751 restraints weight = 136893.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.047326 restraints weight = 86954.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.047581 restraints weight = 78936.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.047788 restraints weight = 65829.048| |-----------------------------------------------------------------------------| r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.5344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 21423 Z= 0.183 Angle : 0.630 13.992 29035 Z= 0.330 Chirality : 0.041 0.194 3290 Planarity : 0.004 0.087 3812 Dihedral : 6.881 136.029 3150 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.15 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.17), residues: 2649 helix: 1.36 (0.13), residues: 1527 sheet: -0.92 (0.29), residues: 310 loop : -0.64 (0.24), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 164 TYR 0.015 0.002 TYR D 344 PHE 0.024 0.002 PHE C 259 TRP 0.018 0.002 TRP B 48 HIS 0.004 0.001 HIS E 29 Details of bonding type rmsd covalent geometry : bond 0.00370 (21423) covalent geometry : angle 0.62959 (29035) hydrogen bonds : bond 0.03338 ( 1226) hydrogen bonds : angle 4.56227 ( 3570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2967.27 seconds wall clock time: 52 minutes 29.61 seconds (3149.61 seconds total)