Starting phenix.real_space_refine on Sat Jul 4 13:46:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7t20_25607/07_2026/7t20_25607.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t20_25607/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7t20_25607/07_2026/7t20_25607.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7t20_25607/07_2026/7t20_25607.cif" model { file = "/net/cci-nas-00/data/ceres_data/7t20_25607/07_2026/7t20_25607.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t20_25607/07_2026/7t20_25607.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t20_25607/07_2026/7t20_25607.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t20_25607/07_2026/7t20_25607.map" } 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-6108/lib/python3.11/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: 5.00, 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: 1.74 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.86 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: 3.49 Time building geometry restraints manager: 2.34 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: 12963 31.79 - 63.58: 211 63.58 - 95.38: 6 95.38 - 127.17: 0 127.17 - 158.96: 1 Dihedral angle restraints: 13181 sinusoidal: 5477 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 13178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2774 0.055 - 0.110: 482 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: 1.920 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: 0.070 Set scattering table: 0.040 Process input model: 20.730 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 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= 0.219 Angle : 0.641 19.484 29035 Z= 0.371 Chirality : 0.039 0.275 3290 Planarity : 0.004 0.052 3812 Dihedral : 11.191 158.959 8189 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/Z covalent geometry : bond 0.00395 / 0.22 (21423) covalent geometry : angle 0.64150 / 0.37 (29035) hydrogen bonds : bond 0.13716 / 9.43 ( 1226) hydrogen bonds : angle 5.27944 / 3.77 ( 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 : 0.826 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: 0.1559 time to fit residues: 110.0169 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 : 0.891 ------------------------------------------------------------------------------- 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... 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 = 0.3574 r_free = 0.3574 target = 0.069103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.054681 restraints weight = 227360.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.056106 restraints weight = 127870.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.056983 restraints weight = 77645.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.057092 restraints weight = 69273.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.057288 restraints weight = 57611.040| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21423 Z= 0.179 Angle : 0.608 9.518 29035 Z= 0.321 Chirality : 0.041 0.218 3290 Planarity : 0.005 0.101 3812 Dihedral : 6.467 176.450 3038 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.13 % Favored : 96.75 % Rotamer: Outliers : 0.35 % Allowed : 2.26 % Favored : 97.38 % 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: 1.13 (0.17), residues: 2649 helix: 1.97 (0.13), residues: 1510 sheet: -1.82 (0.27), residues: 309 loop : -0.43 (0.23), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 285 TYR 0.031 0.002 TYR A 344 PHE 0.026 0.002 PHE A 460 TRP 0.028 0.002 TRP B 457 HIS 0.012 0.002 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 (21423) covalent geometry : angle 0.60841 / 0.32 (29035) hydrogen bonds : bond 0.03708 / 2.56 ( 1226) hydrogen bonds : angle 4.49345 / 3.28 ( 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 303 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 295 time to evaluate : 0.833 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: A 242 MET cc_start: 0.9724 (tpt) cc_final: 0.9427 (tpp) REVERT: A 339 LEU cc_start: 0.9587 (tp) cc_final: 0.9238 (pp) REVERT: A 341 MET cc_start: 0.7846 (ttt) cc_final: 0.5756 (ppp) REVERT: B 172 ARG cc_start: 0.7082 (tpt170) cc_final: 0.6827 (tpt170) REVERT: B 235 MET cc_start: 0.4239 (mmt) cc_final: 0.4014 (mmm) REVERT: B 270 MET cc_start: 0.9550 (mtm) cc_final: 0.9228 (mmm) REVERT: B 347 LEU cc_start: 0.9377 (mm) cc_final: 0.8933 (tt) REVERT: B 348 MET cc_start: 0.9427 (mmm) cc_final: 0.9060 (tpt) REVERT: D 361 ILE cc_start: 0.9655 (OUTLIER) cc_final: 0.9242 (mp) REVERT: E 242 MET cc_start: 0.8176 (ttp) cc_final: 0.7902 (ptm) REVERT: F 105 TYR cc_start: 0.9272 (t80) cc_final: 0.9045 (t80) REVERT: F 106 LEU cc_start: 0.9892 (mt) cc_final: 0.9567 (mt) REVERT: F 159 ASP cc_start: 0.9527 (m-30) cc_final: 0.9266 (p0) REVERT: F 240 PHE cc_start: 0.9838 (t80) cc_final: 0.9537 (t80) REVERT: F 242 MET cc_start: 0.8536 (ttp) cc_final: 0.8143 (ptm) outliers start: 8 outliers final: 5 residues processed: 302 average time/residue: 0.1700 time to fit residues: 76.4868 Evaluate side-chains 210 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 204 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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: 20.0000 chunk 247 optimal weight: 10.0000 chunk 167 optimal weight: 20.0000 chunk 244 optimal weight: 4.9990 chunk 255 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 184 optimal weight: 6.9990 chunk 188 optimal weight: 0.0980 chunk 224 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 40.0000 overall best weight: 4.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN ** E 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.067630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.053584 restraints weight = 229901.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.054740 restraints weight = 126422.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.055244 restraints weight = 77694.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.055478 restraints weight = 70803.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.055833 restraints weight = 58481.870| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 21423 Z= 0.147 Angle : 0.552 10.577 29035 Z= 0.290 Chirality : 0.040 0.221 3290 Planarity : 0.004 0.052 3812 Dihedral : 6.290 170.437 3038 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.13 % Favored : 96.83 % Rotamer: Outliers : 0.09 % Allowed : 1.95 % 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: 1.09 (0.17), residues: 2649 helix: 1.87 (0.13), residues: 1515 sheet: -1.64 (0.26), residues: 324 loop : -0.34 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 387 TYR 0.020 0.001 TYR A 344 PHE 0.014 0.002 PHE C 60 TRP 0.020 0.001 TRP A 48 HIS 0.004 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (21423) covalent geometry : angle 0.55232 / 0.29 (29035) hydrogen bonds : bond 0.03355 / 2.31 ( 1226) hydrogen bonds : angle 4.32520 / 3.17 ( 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 285 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 283 time to evaluate : 0.872 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: A 242 MET cc_start: 0.9721 (tpt) cc_final: 0.9393 (tpp) REVERT: A 339 LEU cc_start: 0.9584 (tp) cc_final: 0.9300 (pp) REVERT: A 341 MET cc_start: 0.7713 (ttt) cc_final: 0.6009 (ppp) REVERT: B 172 ARG cc_start: 0.6969 (tpt170) cc_final: 0.6509 (tpt170) REVERT: B 347 LEU cc_start: 0.9275 (mm) cc_final: 0.8860 (tt) REVERT: B 348 MET cc_start: 0.9491 (mmm) cc_final: 0.9201 (tpt) REVERT: C 415 ILE cc_start: 0.9809 (mt) cc_final: 0.9541 (mp) REVERT: D 38 LEU cc_start: 0.9863 (mt) cc_final: 0.9639 (mt) REVERT: D 105 TYR cc_start: 0.8678 (t80) cc_final: 0.8332 (t80) REVERT: D 281 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.8143 (pp30) REVERT: D 348 MET cc_start: 0.9713 (mmm) cc_final: 0.9260 (tpt) REVERT: D 410 GLN cc_start: 0.9336 (mt0) cc_final: 0.9005 (mm-40) REVERT: E 142 ILE cc_start: 0.9776 (mm) cc_final: 0.9477 (mm) REVERT: E 263 MET cc_start: 0.8691 (mmp) cc_final: 0.8250 (mmm) REVERT: E 348 MET cc_start: 0.8875 (tpt) cc_final: 0.8544 (tpt) REVERT: F 105 TYR cc_start: 0.9220 (t80) cc_final: 0.8904 (t80) REVERT: F 242 MET cc_start: 0.8318 (ttp) cc_final: 0.8028 (ptm) REVERT: F 382 LEU cc_start: 0.7992 (mt) cc_final: 0.7791 (mt) REVERT: F 418 ILE cc_start: 0.9594 (mp) cc_final: 0.9058 (mp) outliers start: 2 outliers final: 0 residues processed: 284 average time/residue: 0.1674 time to fit residues: 70.3361 Evaluate side-chains 210 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.837 ------------------------------------------------------------------------------- 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: 50.0000 chunk 229 optimal weight: 0.3980 chunk 51 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 100 optimal weight: 5.9990 chunk 203 optimal weight: 5.9990 overall best weight: 3.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 ASN D 252 GLN D 281 GLN E 140 ASN E 410 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.040262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.026875 restraints weight = 226704.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.027689 restraints weight = 178605.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.028310 restraints weight = 148722.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.028836 restraints weight = 129278.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.029225 restraints weight = 115086.683| |-----------------------------------------------------------------------------| r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 21423 Z= 0.133 Angle : 0.549 10.153 29035 Z= 0.286 Chirality : 0.040 0.215 3290 Planarity : 0.005 0.111 3812 Dihedral : 6.241 166.632 3038 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 0.09 % Allowed : 2.26 % 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: 1.04 (0.17), residues: 2649 helix: 1.79 (0.13), residues: 1514 sheet: -1.47 (0.27), residues: 313 loop : -0.41 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 152 TYR 0.013 0.001 TYR B 344 PHE 0.034 0.002 PHE C 259 TRP 0.010 0.001 TRP A 48 HIS 0.004 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (21423) covalent geometry : angle 0.54870 / 0.29 (29035) hydrogen bonds : bond 0.03129 / 2.14 ( 1226) hydrogen bonds : angle 4.26822 / 3.13 ( 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 270 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 268 time to evaluate : 0.864 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 60 PHE cc_start: 0.9404 (m-10) cc_final: 0.9185 (m-80) REVERT: A 242 MET cc_start: 0.9816 (tpt) cc_final: 0.9438 (tpp) REVERT: A 339 LEU cc_start: 0.9608 (tp) cc_final: 0.9374 (pp) REVERT: A 341 MET cc_start: 0.7398 (ttt) cc_final: 0.5775 (ppp) REVERT: B 235 MET cc_start: 0.4869 (mmm) cc_final: 0.4522 (mmm) REVERT: B 348 MET cc_start: 0.9510 (mmm) cc_final: 0.8996 (tpt) REVERT: C 235 MET cc_start: 0.9620 (mmp) cc_final: 0.9415 (mmm) REVERT: C 242 MET cc_start: 0.9640 (tpt) cc_final: 0.9428 (tpp) REVERT: C 415 ILE cc_start: 0.9530 (mt) cc_final: 0.9196 (mp) REVERT: C 416 MET cc_start: 0.9572 (tpt) cc_final: 0.9191 (tpp) REVERT: D 105 TYR cc_start: 0.9036 (t80) cc_final: 0.8618 (t80) REVERT: D 226 LEU cc_start: 0.9539 (tp) cc_final: 0.9196 (tp) REVERT: D 240 PHE cc_start: 0.9745 (t80) cc_final: 0.9441 (t80) REVERT: D 281 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8903 (pp30) REVERT: D 348 MET cc_start: 0.9604 (mmm) cc_final: 0.9364 (tpt) REVERT: D 376 ASN cc_start: 0.9844 (t0) cc_final: 0.9637 (m-40) REVERT: E 60 PHE cc_start: 0.9510 (m-80) cc_final: 0.9256 (m-80) REVERT: E 263 MET cc_start: 0.9035 (mmp) cc_final: 0.8762 (mmm) REVERT: E 348 MET cc_start: 0.8936 (tpt) cc_final: 0.8516 (tpt) REVERT: E 414 LEU cc_start: 0.9356 (mt) cc_final: 0.9042 (mt) REVERT: F 105 TYR cc_start: 0.9566 (t80) cc_final: 0.9201 (t80) REVERT: F 242 MET cc_start: 0.9123 (ttp) cc_final: 0.8881 (ptm) REVERT: F 418 ILE cc_start: 0.9601 (mp) cc_final: 0.9346 (mp) outliers start: 2 outliers final: 1 residues processed: 270 average time/residue: 0.1695 time to fit residues: 68.8114 Evaluate side-chains 202 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 200 time to evaluate : 0.814 ------------------------------------------------------------------------------- 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: 3.9990 chunk 17 optimal weight: 9.9990 chunk 2 optimal weight: 20.0000 chunk 64 optimal weight: 0.0270 chunk 202 optimal weight: 9.9990 chunk 209 optimal weight: 0.1980 chunk 174 optimal weight: 3.9990 chunk 23 optimal weight: 40.0000 chunk 160 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 overall best weight: 1.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 ASN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.040590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.027098 restraints weight = 221695.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.027934 restraints weight = 174788.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2674 r_free = 0.2674 target = 0.028593 restraints weight = 145253.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.029087 restraints weight = 125663.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.029518 restraints weight = 112396.265| |-----------------------------------------------------------------------------| r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 21423 Z= 0.121 Angle : 0.554 13.362 29035 Z= 0.285 Chirality : 0.041 0.446 3290 Planarity : 0.004 0.074 3812 Dihedral : 6.188 164.698 3038 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.90 % Rotamer: Outliers : 0.04 % Allowed : 1.24 % Favored : 98.71 % 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: 1.06 (0.17), residues: 2649 helix: 1.80 (0.13), residues: 1514 sheet: -1.37 (0.27), residues: 319 loop : -0.42 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 63 TYR 0.015 0.001 TYR B 344 PHE 0.031 0.001 PHE C 259 TRP 0.022 0.001 TRP A 457 HIS 0.003 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (21423) covalent geometry : angle 0.55387 / 0.29 (29035) hydrogen bonds : bond 0.03104 / 2.08 ( 1226) hydrogen bonds : angle 4.27879 / 3.12 ( 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 259 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 258 time to evaluate : 0.773 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: A 242 MET cc_start: 0.9831 (tpt) cc_final: 0.9438 (tpp) REVERT: A 339 LEU cc_start: 0.9583 (tp) cc_final: 0.9363 (pp) REVERT: A 341 MET cc_start: 0.7263 (ttt) cc_final: 0.5790 (ppp) REVERT: B 235 MET cc_start: 0.4619 (mmt) cc_final: 0.4310 (mmm) REVERT: B 348 MET cc_start: 0.9495 (mmm) cc_final: 0.9213 (tpt) REVERT: C 226 LEU cc_start: 0.9551 (tp) cc_final: 0.9228 (mt) REVERT: C 235 MET cc_start: 0.9597 (mmp) cc_final: 0.9373 (mmm) REVERT: C 242 MET cc_start: 0.9623 (tpt) cc_final: 0.9399 (tpp) REVERT: C 415 ILE cc_start: 0.9547 (mt) cc_final: 0.9240 (mp) REVERT: C 416 MET cc_start: 0.9569 (tpt) cc_final: 0.9267 (tpp) REVERT: D 105 TYR cc_start: 0.9043 (t80) cc_final: 0.8625 (t80) REVERT: D 226 LEU cc_start: 0.9523 (tp) cc_final: 0.9218 (tp) REVERT: D 240 PHE cc_start: 0.9743 (t80) cc_final: 0.9480 (t80) REVERT: D 263 MET cc_start: 0.8391 (mpp) cc_final: 0.7948 (mpp) REVERT: D 281 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.8881 (pp30) REVERT: D 348 MET cc_start: 0.9652 (mmm) cc_final: 0.9364 (tpt) REVERT: D 376 ASN cc_start: 0.9833 (t0) cc_final: 0.9629 (m-40) REVERT: E 60 PHE cc_start: 0.9486 (m-80) cc_final: 0.9229 (m-80) REVERT: E 263 MET cc_start: 0.9032 (mmp) cc_final: 0.8715 (mmm) REVERT: E 348 MET cc_start: 0.8873 (tpt) cc_final: 0.8455 (tpt) REVERT: E 414 LEU cc_start: 0.9285 (mt) cc_final: 0.9009 (mt) REVERT: F 42 MET cc_start: 0.7864 (ttp) cc_final: 0.7556 (tmm) REVERT: F 105 TYR cc_start: 0.9594 (t80) cc_final: 0.9235 (t80) REVERT: F 106 LEU cc_start: 0.9645 (mt) cc_final: 0.9432 (mt) REVERT: F 418 ILE cc_start: 0.9558 (mp) cc_final: 0.9293 (mp) outliers start: 1 outliers final: 0 residues processed: 259 average time/residue: 0.1499 time to fit residues: 59.1393 Evaluate side-chains 193 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 0.823 ------------------------------------------------------------------------------- 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: 3.9990 chunk 178 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 234 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 chunk 187 optimal weight: 3.9990 chunk 218 optimal weight: 20.0000 chunk 108 optimal weight: 4.9990 chunk 251 optimal weight: 9.9990 chunk 232 optimal weight: 0.5980 chunk 3 optimal weight: 8.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 281 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.065635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.051599 restraints weight = 232352.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.053398 restraints weight = 120680.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.053774 restraints weight = 72324.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.053834 restraints weight = 66691.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.054235 restraints weight = 56501.365| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.3803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21423 Z= 0.137 Angle : 0.556 12.007 29035 Z= 0.288 Chirality : 0.040 0.317 3290 Planarity : 0.004 0.074 3812 Dihedral : 6.200 159.099 3038 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.44 % Favored : 96.49 % Rotamer: Outliers : 0.13 % Allowed : 1.60 % Favored : 98.27 % 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: 1.03 (0.17), residues: 2649 helix: 1.77 (0.13), residues: 1512 sheet: -1.30 (0.27), residues: 330 loop : -0.44 (0.23), residues: 807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 93 TYR 0.016 0.001 TYR D 344 PHE 0.020 0.002 PHE F 240 TRP 0.019 0.001 TRP A 457 HIS 0.004 0.001 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 (21423) covalent geometry : angle 0.55613 / 0.29 (29035) hydrogen bonds : bond 0.03118 / 2.09 ( 1226) hydrogen bonds : angle 4.28891 / 3.11 ( 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 253 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 250 time to evaluate : 0.621 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: A 242 MET cc_start: 0.9764 (tpt) cc_final: 0.9412 (tpp) REVERT: A 339 LEU cc_start: 0.9597 (tp) cc_final: 0.9356 (pp) REVERT: A 341 MET cc_start: 0.7557 (ttt) cc_final: 0.5980 (ppp) REVERT: B 348 MET cc_start: 0.9510 (mmm) cc_final: 0.9206 (tpt) REVERT: C 242 MET cc_start: 0.9677 (tpt) cc_final: 0.9469 (tpp) REVERT: C 415 ILE cc_start: 0.9644 (mt) cc_final: 0.9378 (mp) REVERT: D 105 TYR cc_start: 0.8738 (t80) cc_final: 0.8401 (t80) REVERT: D 240 PHE cc_start: 0.9767 (t80) cc_final: 0.9560 (t80) REVERT: D 281 GLN cc_start: 0.8833 (OUTLIER) cc_final: 0.8310 (pp30) REVERT: D 348 MET cc_start: 0.9755 (mmm) cc_final: 0.9430 (tpt) REVERT: E 263 MET cc_start: 0.8224 (mmp) cc_final: 0.7505 (mmm) REVERT: E 268 ILE cc_start: 0.9751 (mm) cc_final: 0.9143 (mm) REVERT: E 271 ARG cc_start: 0.9546 (mtt180) cc_final: 0.9266 (mtt180) REVERT: E 301 MET cc_start: 0.9680 (ptp) cc_final: 0.9428 (ptp) REVERT: E 348 MET cc_start: 0.8786 (tpt) cc_final: 0.8419 (tpt) REVERT: F 105 TYR cc_start: 0.9290 (t80) cc_final: 0.8979 (t80) REVERT: F 106 LEU cc_start: 0.9665 (mt) cc_final: 0.9406 (mt) REVERT: F 418 ILE cc_start: 0.9541 (mp) cc_final: 0.9156 (mp) outliers start: 3 outliers final: 0 residues processed: 253 average time/residue: 0.1580 time to fit residues: 60.1812 Evaluate side-chains 187 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 186 time to evaluate : 0.776 ------------------------------------------------------------------------------- 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: 30.0000 chunk 50 optimal weight: 6.9990 chunk 241 optimal weight: 8.9990 chunk 161 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 234 optimal weight: 8.9990 chunk 227 optimal weight: 20.0000 chunk 132 optimal weight: 0.0470 chunk 61 optimal weight: 0.3980 chunk 117 optimal weight: 0.3980 overall best weight: 1.5680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3551 r_free = 0.3551 target = 0.067552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.053381 restraints weight = 227805.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.054634 restraints weight = 122804.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.055177 restraints weight = 78504.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.055381 restraints weight = 68220.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.055715 restraints weight = 56253.988| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 21423 Z= 0.108 Angle : 0.551 10.799 29035 Z= 0.281 Chirality : 0.041 0.282 3290 Planarity : 0.004 0.055 3812 Dihedral : 6.157 157.312 3038 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.10 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % 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: 1.06 (0.17), residues: 2649 helix: 1.76 (0.13), residues: 1520 sheet: -1.17 (0.27), residues: 331 loop : -0.43 (0.24), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG F 93 TYR 0.015 0.001 TYR D 344 PHE 0.032 0.002 PHE C 259 TRP 0.015 0.001 TRP A 457 HIS 0.002 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (21423) covalent geometry : angle 0.55122 / 0.28 (29035) hydrogen bonds : bond 0.02993 / 2.02 ( 1226) hydrogen bonds : angle 4.24016 / 3.09 ( 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 253 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 0.834 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: 0.9789 (tpt) cc_final: 0.9431 (tpp) REVERT: A 339 LEU cc_start: 0.9579 (tp) cc_final: 0.9349 (pp) REVERT: A 341 MET cc_start: 0.7433 (ttt) cc_final: 0.5956 (ppp) REVERT: B 235 MET cc_start: 0.3080 (mmm) cc_final: 0.2641 (mmm) REVERT: B 348 MET cc_start: 0.9513 (mmm) cc_final: 0.9191 (tpt) REVERT: C 226 LEU cc_start: 0.9739 (tp) cc_final: 0.9523 (mt) REVERT: C 242 MET cc_start: 0.9676 (tpt) cc_final: 0.9456 (tpp) REVERT: D 105 TYR cc_start: 0.8752 (t80) cc_final: 0.8417 (t80) REVERT: D 269 MET cc_start: 0.9670 (ttm) cc_final: 0.9445 (ttm) REVERT: D 348 MET cc_start: 0.9743 (mmm) cc_final: 0.9438 (tpp) REVERT: D 417 PHE cc_start: 0.9382 (m-80) cc_final: 0.9179 (m-80) REVERT: E 263 MET cc_start: 0.8102 (mmp) cc_final: 0.7616 (mmm) REVERT: E 268 ILE cc_start: 0.9713 (mm) cc_final: 0.9323 (pt) REVERT: E 271 ARG cc_start: 0.9468 (mtt180) cc_final: 0.9252 (mtt180) REVERT: E 301 MET cc_start: 0.9653 (ptp) cc_final: 0.9381 (ptp) REVERT: E 348 MET cc_start: 0.8723 (tpt) cc_final: 0.8472 (tpt) REVERT: F 105 TYR cc_start: 0.9300 (t80) cc_final: 0.8984 (t80) REVERT: F 240 PHE cc_start: 0.9857 (t80) cc_final: 0.9655 (t80) REVERT: F 270 MET cc_start: 0.9485 (ttt) cc_final: 0.8776 (tmm) outliers start: 0 outliers final: 0 residues processed: 253 average time/residue: 0.1639 time to fit residues: 63.2149 Evaluate side-chains 190 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 0.757 ------------------------------------------------------------------------------- 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: 6.9990 chunk 243 optimal weight: 9.9990 chunk 34 optimal weight: 30.0000 chunk 191 optimal weight: 10.0000 chunk 225 optimal weight: 0.2980 chunk 116 optimal weight: 20.0000 chunk 111 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 193 optimal weight: 9.9990 overall best weight: 5.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 112 ASN B 140 ASN ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 ASN E 247 ASN E 454 ASN ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.062329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.048698 restraints weight = 239523.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.049805 restraints weight = 140480.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.050475 restraints weight = 84529.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.050635 restraints weight = 80794.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.050886 restraints weight = 65141.741| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21423 Z= 0.185 Angle : 0.621 12.286 29035 Z= 0.324 Chirality : 0.041 0.262 3290 Planarity : 0.004 0.045 3812 Dihedral : 6.154 145.988 3038 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 18.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.85 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: 0.92 (0.17), residues: 2649 helix: 1.62 (0.13), residues: 1522 sheet: -0.96 (0.28), residues: 327 loop : -0.56 (0.24), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 127 TYR 0.016 0.002 TYR D 344 PHE 0.025 0.002 PHE E 60 TRP 0.014 0.001 TRP A 457 HIS 0.005 0.002 HIS A 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.19 (21423) covalent geometry : angle 0.62119 / 0.32 (29035) hydrogen bonds : bond 0.03243 / 2.21 ( 1226) hydrogen bonds : angle 4.44206 / 3.24 ( 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 235 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.862 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 242 MET cc_start: 0.9794 (tpt) cc_final: 0.9430 (tpp) REVERT: A 341 MET cc_start: 0.7521 (ttt) cc_final: 0.5850 (ppp) REVERT: B 235 MET cc_start: 0.3775 (mmm) cc_final: 0.3249 (mmm) REVERT: B 270 MET cc_start: 0.9564 (mtm) cc_final: 0.9349 (tmm) REVERT: B 348 MET cc_start: 0.9496 (mmm) cc_final: 0.9294 (tmm) REVERT: C 242 MET cc_start: 0.9636 (tpt) cc_final: 0.9414 (tpp) REVERT: D 105 TYR cc_start: 0.8799 (t80) cc_final: 0.8471 (t80) REVERT: D 240 PHE cc_start: 0.9765 (t80) cc_final: 0.9543 (t80) REVERT: D 348 MET cc_start: 0.9749 (mmm) cc_final: 0.8563 (mmm) REVERT: D 415 ILE cc_start: 0.9887 (mp) cc_final: 0.9675 (pt) REVERT: D 417 PHE cc_start: 0.9458 (m-80) cc_final: 0.9173 (m-10) REVERT: E 242 MET cc_start: 0.8228 (tmm) cc_final: 0.7553 (tmm) REVERT: E 271 ARG cc_start: 0.9426 (mtt180) cc_final: 0.9127 (ptm-80) REVERT: E 301 MET cc_start: 0.9663 (ptp) cc_final: 0.9381 (ptp) REVERT: F 105 TYR cc_start: 0.9336 (t80) cc_final: 0.9045 (t80) REVERT: F 106 LEU cc_start: 0.9766 (mt) cc_final: 0.9459 (mt) REVERT: F 235 MET cc_start: 0.8462 (ttt) cc_final: 0.7933 (mtp) REVERT: F 240 PHE cc_start: 0.9860 (t80) cc_final: 0.9653 (t80) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.1588 time to fit residues: 57.3719 Evaluate side-chains 178 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 178 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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: 6.9990 chunk 244 optimal weight: 6.9990 chunk 130 optimal weight: 30.0000 chunk 202 optimal weight: 6.9990 chunk 89 optimal weight: 5.9990 chunk 42 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 146 optimal weight: 1.9990 chunk 154 optimal weight: 7.9990 chunk 155 optimal weight: 40.0000 chunk 215 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 443 ASN ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 ASN ** F 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.061331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.047892 restraints weight = 240198.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.048955 restraints weight = 136036.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.049491 restraints weight = 85819.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.049662 restraints weight = 78157.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.049886 restraints weight = 65951.736| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7354 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21423 Z= 0.177 Angle : 0.616 11.938 29035 Z= 0.322 Chirality : 0.041 0.245 3290 Planarity : 0.004 0.052 3812 Dihedral : 6.226 138.356 3038 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.66 % 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: 0.79 (0.17), residues: 2649 helix: 1.46 (0.13), residues: 1521 sheet: -0.91 (0.28), residues: 325 loop : -0.55 (0.24), residues: 803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 366 TYR 0.015 0.002 TYR D 344 PHE 0.021 0.002 PHE C 60 TRP 0.014 0.002 TRP A 457 HIS 0.004 0.001 HIS E 29 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.18 (21423) covalent geometry : angle 0.61619 / 0.32 (29035) hydrogen bonds : bond 0.03316 / 2.25 ( 1226) hydrogen bonds : angle 4.46332 / 3.26 ( 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 : 0.837 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 242 MET cc_start: 0.9777 (tpt) cc_final: 0.9393 (tpp) REVERT: A 341 MET cc_start: 0.7677 (ttt) cc_final: 0.6105 (ppp) REVERT: B 270 MET cc_start: 0.9546 (mtm) cc_final: 0.9317 (tmm) REVERT: B 348 MET cc_start: 0.9488 (mmm) cc_final: 0.9223 (tpt) REVERT: C 242 MET cc_start: 0.9609 (tpt) cc_final: 0.9405 (tpp) REVERT: D 105 TYR cc_start: 0.8776 (t80) cc_final: 0.8572 (t80) REVERT: D 417 PHE cc_start: 0.9426 (m-80) cc_final: 0.9198 (m-80) REVERT: E 301 MET cc_start: 0.9628 (ptp) cc_final: 0.9349 (ptp) REVERT: E 348 MET cc_start: 0.9078 (tpt) cc_final: 0.8742 (tpt) REVERT: F 105 TYR cc_start: 0.9295 (t80) cc_final: 0.9019 (t80) REVERT: F 235 MET cc_start: 0.8536 (ttt) cc_final: 0.8039 (mtp) REVERT: F 240 PHE cc_start: 0.9845 (t80) cc_final: 0.9620 (t80) outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1402 time to fit residues: 49.5858 Evaluate side-chains 167 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 167 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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: 3.9990 chunk 256 optimal weight: 40.0000 chunk 246 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 212 optimal weight: 7.9990 chunk 240 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 167 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 257 optimal weight: 20.0000 chunk 58 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 454 ASN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3423 r_free = 0.3423 target = 0.061007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.047403 restraints weight = 241962.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.049142 restraints weight = 125432.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.049363 restraints weight = 74625.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.049589 restraints weight = 64921.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.049665 restraints weight = 58071.240| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21423 Z= 0.169 Angle : 0.615 12.500 29035 Z= 0.319 Chirality : 0.041 0.194 3290 Planarity : 0.004 0.054 3812 Dihedral : 6.275 135.882 3038 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.78 (0.17), residues: 2649 helix: 1.48 (0.13), residues: 1514 sheet: -1.00 (0.29), residues: 303 loop : -0.56 (0.23), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 324 TYR 0.019 0.002 TYR F 424 PHE 0.023 0.002 PHE B 240 TRP 0.014 0.002 TRP B 48 HIS 0.006 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.17 (21423) covalent geometry : angle 0.61532 / 0.32 (29035) hydrogen bonds : bond 0.03263 / 2.22 ( 1226) hydrogen bonds : angle 4.48913 / 3.27 ( 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 225 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.850 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: A 242 MET cc_start: 0.9764 (tpt) cc_final: 0.9378 (tpp) REVERT: A 341 MET cc_start: 0.7920 (ttt) cc_final: 0.6207 (ppp) REVERT: B 348 MET cc_start: 0.9481 (mmm) cc_final: 0.9272 (tpt) REVERT: C 164 ARG cc_start: 0.9661 (mpt180) cc_final: 0.9441 (mmt-90) REVERT: D 415 ILE cc_start: 0.9880 (mp) cc_final: 0.9655 (pt) REVERT: D 417 PHE cc_start: 0.9435 (m-80) cc_final: 0.9158 (m-10) REVERT: E 301 MET cc_start: 0.9638 (ptp) cc_final: 0.9357 (ptp) REVERT: F 105 TYR cc_start: 0.9307 (t80) cc_final: 0.9030 (t80) REVERT: F 235 MET cc_start: 0.8291 (ttt) cc_final: 0.8080 (tpt) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1582 time to fit residues: 54.9757 Evaluate side-chains 168 residues out of total 2256 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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: 3.9990 chunk 92 optimal weight: 20.0000 chunk 152 optimal weight: 10.0000 chunk 60 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 222 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 165 optimal weight: 5.9990 chunk 110 optimal weight: 0.4980 chunk 158 optimal weight: 9.9990 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 454 ASN ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 281 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 281 GLN ** F 462 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.037189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2531 r_free = 0.2531 target = 0.024598 restraints weight = 241089.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.025332 restraints weight = 191086.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.025909 restraints weight = 159367.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.026345 restraints weight = 138602.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.026700 restraints weight = 124348.639| |-----------------------------------------------------------------------------| r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 21423 Z= 0.152 Angle : 0.597 11.902 29035 Z= 0.309 Chirality : 0.041 0.179 3290 Planarity : 0.004 0.053 3812 Dihedral : 6.316 135.527 3038 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 0.79 (0.17), residues: 2649 helix: 1.49 (0.13), residues: 1519 sheet: -0.99 (0.29), residues: 310 loop : -0.59 (0.23), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 349 TYR 0.015 0.002 TYR D 344 PHE 0.031 0.002 PHE C 259 TRP 0.015 0.002 TRP B 48 HIS 0.006 0.001 HIS D 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (21423) covalent geometry : angle 0.59678 / 0.31 (29035) hydrogen bonds : bond 0.03173 / 2.15 ( 1226) hydrogen bonds : angle 4.45182 / 3.24 ( 3570) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3118.25 seconds wall clock time: 55 minutes 3.52 seconds (3303.52 seconds total)