Starting phenix.real_space_refine on Sun Aug 9 01:41:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jay_36138/08_2026/8jay_36138.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jay_36138/08_2026/8jay_36138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jay_36138/08_2026/8jay_36138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jay_36138/08_2026/8jay_36138.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jay_36138/08_2026/8jay_36138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jay_36138/08_2026/8jay_36138.map" } resolution = 4.2 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= 0.025 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 166 5.49 5 Mg 4 5.21 5 S 88 5.16 5 C 20152 2.51 5 N 5403 2.21 5 O 6169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 31982 Number of models: 1 Model: "" Number of chains: 20 Chain: "C" Number of atoms: 3626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3626 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 25, 'TRANS': 423} Chain breaks: 1 Chain: "A" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3618 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 25, 'TRANS': 422} Chain breaks: 1 Chain: "D" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3531 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 14, 'TRANS': 407} Chain: "B" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3531 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 14, 'TRANS': 407} Chain: "I" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3618 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 25, 'TRANS': 422} Chain breaks: 1 Chain: "J" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3531 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 14, 'TRANS': 407} Chain: "M" Number of atoms: 3618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3618 Classifications: {'peptide': 448} Link IDs: {'PTRANS': 25, 'TRANS': 422} Chain breaks: 1 Chain: "N" Number of atoms: 3531 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3531 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 14, 'TRANS': 407} Chain: "E" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 13, 'RNA': 8} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 20} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "F" Number of atoms: 432 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 21, 432 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "G" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 13, 'RNA': 8} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 20} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "H" Number of atoms: 411 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "K" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 13, 'RNA': 8} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 20} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "L" Number of atoms: 432 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 21, 432 Classifications: {'DNA': 21} Link IDs: {'rna3p': 20} Chain: "O" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 422 Classifications: {'DNA': 13, 'RNA': 8} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 20} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen chiralities: 8 Chain: "P" Number of atoms: 411 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.78, per 1000 atoms: 0.21 Number of scatterers: 31982 At special positions: 0 Unit cell: (119.34, 177.905, 233.155, 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 88 16.00 P 166 15.00 Mg 4 11.99 O 6169 8.00 N 5403 7.00 C 20152 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: 2.79 Conformation dependent library (CDL) restraints added in 1.4 seconds 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6610 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 43 sheets defined 33.6% alpha, 11.2% beta 48 base pairs and 97 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'C' and resid 15 through 17 No H-bonds generated for 'chain 'C' and resid 15 through 17' Processing helix chain 'C' and resid 22 through 30 removed outlier: 3.994A pdb=" N GLY C 26 " --> pdb=" O ASP C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 60 Processing helix chain 'C' and resid 77 through 82 Processing helix chain 'C' and resid 109 through 132 removed outlier: 3.775A pdb=" N ARG C 113 " --> pdb=" O SER C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 215 Processing helix chain 'C' and resid 216 through 218 No H-bonds generated for 'chain 'C' and resid 216 through 218' Processing helix chain 'C' and resid 226 through 230 Processing helix chain 'C' and resid 248 through 265 removed outlier: 4.009A pdb=" N ALA C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP C 254 " --> pdb=" O GLY C 250 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N THR C 258 " --> pdb=" O TRP C 254 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ALA C 259 " --> pdb=" O THR C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 331 through 351 removed outlier: 3.877A pdb=" N ALA C 335 " --> pdb=" O LYS C 331 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS C 336 " --> pdb=" O PRO C 332 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA C 337 " --> pdb=" O LYS C 333 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA C 342 " --> pdb=" O LEU C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 376 removed outlier: 3.961A pdb=" N TRP C 370 " --> pdb=" O ASN C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 451 through 462 Processing helix chain 'C' and resid 477 through 491 removed outlier: 3.957A pdb=" N ARG C 481 " --> pdb=" O PRO C 477 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU C 488 " --> pdb=" O ASN C 484 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE C 489 " --> pdb=" O LYS C 485 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU C 490 " --> pdb=" O ILE C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 507 removed outlier: 4.283A pdb=" N TYR C 506 " --> pdb=" O ALA C 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 22 through 30 Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'A' and resid 109 through 132 Processing helix chain 'A' and resid 205 through 215 removed outlier: 4.492A pdb=" N GLN A 209 " --> pdb=" O GLN A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 218 No H-bonds generated for 'chain 'A' and resid 216 through 218' Processing helix chain 'A' and resid 225 through 230 removed outlier: 4.351A pdb=" N LEU A 229 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 230' Processing helix chain 'A' and resid 248 through 265 removed outlier: 3.558A pdb=" N GLY A 265 " --> pdb=" O TYR A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.964A pdb=" N SER A 345 " --> pdb=" O GLN A 341 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N TYR A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 377 removed outlier: 4.208A pdb=" N GLU A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 377 " --> pdb=" O PHE A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 462 removed outlier: 3.735A pdb=" N VAL A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 456 " --> pdb=" O ILE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 491 removed outlier: 3.685A pdb=" N ARG A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 483 " --> pdb=" O THR A 479 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 488 " --> pdb=" O ASN A 484 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ILE A 489 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 28 Processing helix chain 'D' and resid 46 through 56 removed outlier: 3.820A pdb=" N ILE D 53 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N ARG D 54 " --> pdb=" O GLU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 89 Processing helix chain 'D' and resid 109 through 113 Processing helix chain 'D' and resid 123 through 138 removed outlier: 3.618A pdb=" N GLY D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 158 removed outlier: 4.026A pdb=" N SER D 150 " --> pdb=" O ASP D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 249 Processing helix chain 'D' and resid 257 through 279 removed outlier: 3.784A pdb=" N CYS D 261 " --> pdb=" O ARG D 257 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ASP D 279 " --> pdb=" O LEU D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 304 Processing helix chain 'D' and resid 353 through 366 Processing helix chain 'D' and resid 369 through 385 Processing helix chain 'B' and resid 15 through 29 Processing helix chain 'B' and resid 46 through 54 removed outlier: 3.681A pdb=" N ARG B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 89 Processing helix chain 'B' and resid 125 through 138 Processing helix chain 'B' and resid 219 through 224 removed outlier: 4.133A pdb=" N PHE B 223 " --> pdb=" O GLU B 220 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE B 224 " --> pdb=" O TYR B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 249 Processing helix chain 'B' and resid 258 through 279 removed outlier: 3.611A pdb=" N ASP B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 304 removed outlier: 3.678A pdb=" N LYS B 304 " --> pdb=" O GLU B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 365 Processing helix chain 'B' and resid 369 through 385 Processing helix chain 'I' and resid 15 through 17 No H-bonds generated for 'chain 'I' and resid 15 through 17' Processing helix chain 'I' and resid 22 through 30 Processing helix chain 'I' and resid 46 through 61 removed outlier: 3.675A pdb=" N GLN I 61 " --> pdb=" O LEU I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 82 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 109 through 132 Processing helix chain 'I' and resid 206 through 215 removed outlier: 4.056A pdb=" N LEU I 210 " --> pdb=" O PHE I 206 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N LYS I 211 " --> pdb=" O HIS I 207 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA I 212 " --> pdb=" O ASP I 208 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG I 213 " --> pdb=" O GLN I 209 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU I 214 " --> pdb=" O LEU I 210 " (cutoff:3.500A) Processing helix chain 'I' and resid 216 through 218 No H-bonds generated for 'chain 'I' and resid 216 through 218' Processing helix chain 'I' and resid 225 through 230 removed outlier: 4.149A pdb=" N LEU I 229 " --> pdb=" O ARG I 225 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ALA I 230 " --> pdb=" O GLU I 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 225 through 230' Processing helix chain 'I' and resid 248 through 264 Processing helix chain 'I' and resid 331 through 351 removed outlier: 4.190A pdb=" N LYS I 336 " --> pdb=" O PRO I 332 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ALA I 337 " --> pdb=" O LYS I 333 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU I 338 " --> pdb=" O GLU I 334 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU I 339 " --> pdb=" O ALA I 335 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N GLU I 344 " --> pdb=" O THR I 340 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER I 345 " --> pdb=" O GLN I 341 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR I 346 " --> pdb=" O ALA I 342 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN I 349 " --> pdb=" O SER I 345 " (cutoff:3.500A) Processing helix chain 'I' and resid 366 through 377 removed outlier: 4.111A pdb=" N TRP I 370 " --> pdb=" O ASN I 366 " (cutoff:3.500A) Processing helix chain 'I' and resid 451 through 461 removed outlier: 3.576A pdb=" N VAL I 455 " --> pdb=" O GLU I 451 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N LEU I 460 " --> pdb=" O LEU I 456 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA I 461 " --> pdb=" O LYS I 457 " (cutoff:3.500A) Processing helix chain 'I' and resid 477 through 491 removed outlier: 3.817A pdb=" N ARG I 481 " --> pdb=" O PRO I 477 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU I 488 " --> pdb=" O ASN I 484 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE I 489 " --> pdb=" O LYS I 485 " (cutoff:3.500A) Processing helix chain 'J' and resid 15 through 29 Processing helix chain 'J' and resid 44 through 56 removed outlier: 4.627A pdb=" N GLU J 50 " --> pdb=" O TRP J 46 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG J 54 " --> pdb=" O GLU J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 70 removed outlier: 3.917A pdb=" N ASN J 69 " --> pdb=" O THR J 66 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS J 70 " --> pdb=" O ALA J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 89 removed outlier: 3.696A pdb=" N LEU J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 139 Processing helix chain 'J' and resid 152 through 157 removed outlier: 3.738A pdb=" N ILE J 157 " --> pdb=" O LEU J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 199 through 203 removed outlier: 3.659A pdb=" N THR J 202 " --> pdb=" O ASP J 199 " (cutoff:3.500A) Processing helix chain 'J' and resid 242 through 249 Processing helix chain 'J' and resid 258 through 278 removed outlier: 3.572A pdb=" N GLN J 262 " --> pdb=" O ASN J 258 " (cutoff:3.500A) Processing helix chain 'J' and resid 279 through 281 No H-bonds generated for 'chain 'J' and resid 279 through 281' Processing helix chain 'J' and resid 300 through 302 No H-bonds generated for 'chain 'J' and resid 300 through 302' Processing helix chain 'J' and resid 353 through 366 removed outlier: 3.788A pdb=" N GLN J 357 " --> pdb=" O SER J 353 " (cutoff:3.500A) Processing helix chain 'J' and resid 369 through 384 removed outlier: 3.744A pdb=" N LEU J 384 " --> pdb=" O PHE J 380 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 17 No H-bonds generated for 'chain 'M' and resid 15 through 17' Processing helix chain 'M' and resid 22 through 30 Processing helix chain 'M' and resid 46 through 61 removed outlier: 3.992A pdb=" N GLN M 61 " --> pdb=" O LEU M 57 " (cutoff:3.500A) Processing helix chain 'M' and resid 77 through 83 Processing helix chain 'M' and resid 109 through 132 removed outlier: 3.846A pdb=" N LEU M 117 " --> pdb=" O ARG M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 215 removed outlier: 3.739A pdb=" N LEU M 210 " --> pdb=" O PHE M 206 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 265 removed outlier: 3.603A pdb=" N GLY M 265 " --> pdb=" O TYR M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 331 through 351 removed outlier: 3.902A pdb=" N LYS M 336 " --> pdb=" O PRO M 332 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA M 337 " --> pdb=" O LYS M 333 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER M 345 " --> pdb=" O GLN M 341 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N TYR M 346 " --> pdb=" O ALA M 342 " (cutoff:3.500A) Processing helix chain 'M' and resid 366 through 375 Processing helix chain 'M' and resid 451 through 462 removed outlier: 3.594A pdb=" N VAL M 455 " --> pdb=" O GLU M 451 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU M 460 " --> pdb=" O LEU M 456 " (cutoff:3.500A) Processing helix chain 'M' and resid 478 through 491 removed outlier: 3.870A pdb=" N ALA M 483 " --> pdb=" O THR M 479 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ASN M 484 " --> pdb=" O LEU M 480 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 28 Processing helix chain 'N' and resid 46 through 56 removed outlier: 3.525A pdb=" N GLU N 50 " --> pdb=" O TRP N 46 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ILE N 53 " --> pdb=" O ILE N 49 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N ARG N 54 " --> pdb=" O GLU N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 70 Processing helix chain 'N' and resid 71 through 89 removed outlier: 3.560A pdb=" N LEU N 75 " --> pdb=" O ARG N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 109 through 114 removed outlier: 4.507A pdb=" N ARG N 114 " --> pdb=" O ILE N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 126 through 138 Processing helix chain 'N' and resid 146 through 158 removed outlier: 4.327A pdb=" N SER N 150 " --> pdb=" O ASP N 146 " (cutoff:3.500A) Processing helix chain 'N' and resid 219 through 224 removed outlier: 3.828A pdb=" N PHE N 223 " --> pdb=" O GLU N 220 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ILE N 224 " --> pdb=" O TYR N 221 " (cutoff:3.500A) Processing helix chain 'N' and resid 243 through 248 Processing helix chain 'N' and resid 257 through 279 removed outlier: 3.870A pdb=" N CYS N 261 " --> pdb=" O ARG N 257 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ASP N 279 " --> pdb=" O LEU N 275 " (cutoff:3.500A) Processing helix chain 'N' and resid 300 through 302 No H-bonds generated for 'chain 'N' and resid 300 through 302' Processing helix chain 'N' and resid 354 through 366 Processing helix chain 'N' and resid 369 through 385 Processing sheet with id=AA1, first strand: chain 'C' and resid 397 through 398 removed outlier: 3.707A pdb=" N LEU C 4 " --> pdb=" O PHE D 411 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 12 through 13 Processing sheet with id=AA3, first strand: chain 'C' and resid 92 through 95 removed outlier: 6.727A pdb=" N VAL C 43 " --> pdb=" O LYS C 94 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLY C 42 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 8.196A pdb=" N ILE C 142 " --> pdb=" O GLY C 42 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 44 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N TRP C 139 " --> pdb=" O GLN C 222 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N LEU C 224 " --> pdb=" O TRP C 139 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N VAL C 141 " --> pdb=" O LEU C 224 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 283 through 284 removed outlier: 4.048A pdb=" N VAL C 284 " --> pdb=" O CYS C 299 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 357 through 361 removed outlier: 7.100A pdb=" N VAL C 357 " --> pdb=" O VAL C 384 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N VAL C 386 " --> pdb=" O VAL C 357 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ILE C 359 " --> pdb=" O VAL C 386 " (cutoff:3.500A) removed outlier: 7.780A pdb=" N ILE C 388 " --> pdb=" O ILE C 359 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA C 361 " --> pdb=" O ILE C 388 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 5 through 6 removed outlier: 5.872A pdb=" N ILE A 445 " --> pdb=" O THR A 387 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N THR A 387 " --> pdb=" O ILE A 445 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL A 357 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL A 386 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ILE A 359 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N ILE A 388 " --> pdb=" O ILE A 359 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N CYS A 279 " --> pdb=" O PHE A 358 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N HIS A 360 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N LEU A 281 " --> pdb=" O HIS A 360 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 12 through 13 Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 95 removed outlier: 7.256A pdb=" N GLY A 42 " --> pdb=" O PHE A 140 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 6 removed outlier: 7.634A pdb=" N LYS D 4 " --> pdb=" O CYS D 58 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE D 60 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N PHE D 6 " --> pdb=" O PHE D 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'D' and resid 63 through 64 removed outlier: 3.903A pdb=" N ALA D 98 " --> pdb=" O ILE D 118 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 207 through 208 removed outlier: 3.774A pdb=" N THR D 216 " --> pdb=" O ARG D 186 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG D 186 " --> pdb=" O THR D 216 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 283 through 285 Processing sheet with id=AB5, first strand: chain 'D' and resid 312 through 314 Processing sheet with id=AB6, first strand: chain 'D' and resid 390 through 393 Processing sheet with id=AB7, first strand: chain 'B' and resid 32 through 33 removed outlier: 5.848A pdb=" N ILE B 5 " --> pdb=" O TRP B 33 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N LYS B 4 " --> pdb=" O THR B 57 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS B 59 " --> pdb=" O LYS B 4 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU B 61 " --> pdb=" O PHE B 6 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N SER B 8 " --> pdb=" O LEU B 61 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL B 63 " --> pdb=" O SER B 8 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA B 98 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 176 through 177 Processing sheet with id=AB9, first strand: chain 'B' and resid 207 through 210 Processing sheet with id=AC1, first strand: chain 'B' and resid 283 through 285 Processing sheet with id=AC2, first strand: chain 'B' and resid 390 through 393 Processing sheet with id=AC3, first strand: chain 'I' and resid 5 through 6 removed outlier: 7.116A pdb=" N ILE I 359 " --> pdb=" O VAL I 386 " (cutoff:3.500A) removed outlier: 8.352A pdb=" N ILE I 388 " --> pdb=" O ILE I 359 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ALA I 361 " --> pdb=" O ILE I 388 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 12 through 14 removed outlier: 3.716A pdb=" N GLN I 18 " --> pdb=" O PHE I 14 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 93 through 95 removed outlier: 3.608A pdb=" N LYS I 94 " --> pdb=" O VAL I 43 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLY I 45 " --> pdb=" O LYS I 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 397 through 398 Processing sheet with id=AC7, first strand: chain 'J' and resid 4 through 8 removed outlier: 7.725A pdb=" N LYS J 4 " --> pdb=" O CYS J 58 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N PHE J 60 " --> pdb=" O LYS J 4 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N PHE J 6 " --> pdb=" O PHE J 60 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE J 62 " --> pdb=" O PHE J 6 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N SER J 8 " --> pdb=" O ILE J 62 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N SER J 64 " --> pdb=" O SER J 8 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N LEU J 97 " --> pdb=" O PHE J 60 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ILE J 62 " --> pdb=" O LEU J 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'J' and resid 175 through 177 Processing sheet with id=AC9, first strand: chain 'J' and resid 207 through 210 Processing sheet with id=AD1, first strand: chain 'J' and resid 283 through 285 Processing sheet with id=AD2, first strand: chain 'J' and resid 304 through 305 Processing sheet with id=AD3, first strand: chain 'J' and resid 390 through 391 Processing sheet with id=AD4, first strand: chain 'M' and resid 12 through 13 Processing sheet with id=AD5, first strand: chain 'M' and resid 91 through 95 removed outlier: 7.020A pdb=" N SER M 41 " --> pdb=" O VAL M 92 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N LYS M 94 " --> pdb=" O SER M 41 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N VAL M 43 " --> pdb=" O LYS M 94 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N GLY M 42 " --> pdb=" O PHE M 140 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE M 142 " --> pdb=" O GLY M 42 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL M 44 " --> pdb=" O ILE M 142 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'M' and resid 278 through 279 removed outlier: 3.518A pdb=" N VAL M 357 " --> pdb=" O ASN M 382 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 360 through 361 removed outlier: 3.795A pdb=" N ILE M 388 " --> pdb=" O ALA M 361 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU M 444 " --> pdb=" O THR M 387 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'N' and resid 5 through 7 removed outlier: 3.940A pdb=" N PHE N 6 " --> pdb=" O LYS N 59 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU N 61 " --> pdb=" O PHE N 6 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'N' and resid 63 through 64 Processing sheet with id=AE1, first strand: chain 'N' and resid 164 through 165 Processing sheet with id=AE2, first strand: chain 'N' and resid 169 through 172 Processing sheet with id=AE3, first strand: chain 'N' and resid 184 through 187 Processing sheet with id=AE4, first strand: chain 'N' and resid 283 through 286 removed outlier: 3.917A pdb=" N ARG N 283 " --> pdb=" O TRP N 294 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE N 291 " --> pdb=" O ALA N 325 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ALA N 325 " --> pdb=" O PHE N 291 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR N 293 " --> pdb=" O ILE N 323 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE N 323 " --> pdb=" O TYR N 293 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'N' and resid 283 through 286 removed outlier: 3.917A pdb=" N ARG N 283 " --> pdb=" O TRP N 294 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N PHE N 291 " --> pdb=" O ALA N 325 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ALA N 325 " --> pdb=" O PHE N 291 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TYR N 293 " --> pdb=" O ILE N 323 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE N 323 " --> pdb=" O TYR N 293 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 304 through 305 Processing sheet with id=AE7, first strand: chain 'N' and resid 390 through 394 917 hydrogen bonds defined for protein. 2553 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 119 hydrogen bonds 238 hydrogen bond angles 0 basepair planarities 48 basepair parallelities 97 stacking parallelities Total time for adding SS restraints: 6.25 Time building geometry restraints manager: 3.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8342 1.33 - 1.45: 7103 1.45 - 1.57: 17203 1.57 - 1.69: 324 1.69 - 1.81: 136 Bond restraints: 33108 Sorted by residual: bond pdb=" C3' DA L 14 " pdb=" C2' DA L 14 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.31e+01 bond pdb=" C3' DA P 16 " pdb=" C2' DA P 16 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.27e+01 bond pdb=" C3' A G 3 " pdb=" C2' A G 3 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C3' DA F 14 " pdb=" C2' DA F 14 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3'A DT F 13 " pdb=" C2'A DT F 13 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 ... (remaining 33103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 44836 2.48 - 4.97: 523 4.97 - 7.45: 56 7.45 - 9.94: 8 9.94 - 12.42: 2 Bond angle restraints: 45425 Sorted by residual: angle pdb=" O5' U E 21 " pdb=" C5' U E 21 " pdb=" C4' U E 21 " ideal model delta sigma weight residual 109.40 118.58 -9.18 8.00e-01 1.56e+00 1.32e+02 angle pdb=" O4' U G 17 " pdb=" C1' U G 17 " pdb=" N1 U G 17 " ideal model delta sigma weight residual 108.50 115.33 -6.83 7.00e-01 2.04e+00 9.52e+01 angle pdb=" O4' U O 17 " pdb=" C1' U O 17 " pdb=" N1 U O 17 " ideal model delta sigma weight residual 108.50 115.14 -6.64 7.00e-01 2.04e+00 9.00e+01 angle pdb=" O4' U K 17 " pdb=" C1' U K 17 " pdb=" N1 U K 17 " ideal model delta sigma weight residual 108.50 114.29 -5.79 7.00e-01 2.04e+00 6.85e+01 angle pdb=" O4' U E 17 " pdb=" C1' U E 17 " pdb=" N1 U E 17 " ideal model delta sigma weight residual 108.50 113.76 -5.26 7.00e-01 2.04e+00 5.65e+01 ... (remaining 45420 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.11: 18808 34.11 - 68.23: 775 68.23 - 102.34: 42 102.34 - 136.45: 7 136.45 - 170.57: 5 Dihedral angle restraints: 19637 sinusoidal: 9410 harmonic: 10227 Sorted by residual: dihedral pdb=" CA MET J 92 " pdb=" C MET J 92 " pdb=" N PHE J 93 " pdb=" CA PHE J 93 " ideal model delta harmonic sigma weight residual -180.00 -152.64 -27.36 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA ILE C 242 " pdb=" C ILE C 242 " pdb=" N ARG C 243 " pdb=" CA ARG C 243 " ideal model delta harmonic sigma weight residual -180.00 -152.78 -27.22 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA TYR J 210 " pdb=" C TYR J 210 " pdb=" N LYS J 211 " pdb=" CA LYS J 211 " ideal model delta harmonic sigma weight residual -180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 ... (remaining 19634 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 3583 0.046 - 0.092: 1002 0.092 - 0.138: 295 0.138 - 0.184: 22 0.184 - 0.230: 7 Chirality restraints: 4909 Sorted by residual: chirality pdb=" C1' U K 15 " pdb=" O4' U K 15 " pdb=" C2' U K 15 " pdb=" N1 U K 15 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" C1' U O 1 " pdb=" O4' U O 1 " pdb=" C2' U O 1 " pdb=" N1 U O 1 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" CB ILE J 157 " pdb=" CA ILE J 157 " pdb=" CG1 ILE J 157 " pdb=" CG2 ILE J 157 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 4906 not shown) Planarity restraints: 5180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 231 " -0.025 2.00e-02 2.50e+03 2.95e-02 2.17e+01 pdb=" CG TRP C 231 " 0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP C 231 " -0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP C 231 " 0.011 2.00e-02 2.50e+03 pdb=" NE1 TRP C 231 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 231 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 231 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 231 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 231 " -0.022 2.00e-02 2.50e+03 pdb=" CH2 TRP C 231 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 361 " 0.246 9.50e-02 1.11e+02 1.10e-01 7.45e+00 pdb=" NE ARG D 361 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG D 361 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D 361 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 361 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN I 439 " -0.037 5.00e-02 4.00e+02 5.56e-02 4.95e+00 pdb=" N PRO I 440 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO I 440 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO I 440 " -0.031 5.00e-02 4.00e+02 ... (remaining 5177 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 397 2.58 - 3.16: 26425 3.16 - 3.74: 51620 3.74 - 4.32: 65572 4.32 - 4.90: 103021 Nonbonded interactions: 247035 Sorted by model distance: nonbonded pdb=" OP1 A E 3 " pdb="MG MG E 101 " model vdw 1.999 2.170 nonbonded pdb=" OP1 A K 3 " pdb="MG MG K 101 " model vdw 2.000 2.170 nonbonded pdb=" OP3 U K 1 " pdb="MG MG K 101 " model vdw 2.033 2.170 nonbonded pdb=" OP3 U O 1 " pdb="MG MG M 601 " model vdw 2.051 2.170 nonbonded pdb=" OP2 U G 1 " pdb="MG MG G 101 " model vdw 2.086 2.170 ... (remaining 247030 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 'C' and (resid 1 through 144 or resid 204 through 507)) selection = chain 'I' selection = (chain 'M' and resid 1 through 507) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'J' selection = chain 'N' } ncs_group { reference = (chain 'E' and resid 1 through 21) selection = (chain 'G' and resid 1 through 21) selection = (chain 'K' and resid 1 through 21) selection = chain 'O' } ncs_group { reference = (chain 'F' and resid 4 through 23) selection = chain 'H' selection = (chain 'L' and resid 4 through 23) selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.67 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: 5.060 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: 0.020 Extract box with map and model: 0.540 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 31.190 Find NCS groups from input model: 0.650 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 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 : 0.003 0.043 33108 Z= 0.249 Angle : 0.684 12.423 45425 Z= 0.455 Chirality : 0.047 0.230 4909 Planarity : 0.004 0.110 5180 Dihedral : 17.448 170.565 13027 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -1.79 (0.14), residues: 3457 helix: 0.61 (0.17), residues: 1002 sheet: -1.24 (0.21), residues: 601 loop : -2.28 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 19 TYR 0.019 0.001 TYR B 213 PHE 0.035 0.001 PHE C 245 TRP 0.075 0.002 TRP C 231 HIS 0.006 0.001 HIS N 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.25 (33108) covalent geometry : angle 0.68370 / 0.46 (45425) hydrogen bonds : bond 0.14142 / 9.26 ( 1033) hydrogen bonds : angle 5.73249 / 3.88 ( 2791) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 1.208 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: C 36 ILE cc_start: 0.8370 (mm) cc_final: 0.8153 (tp) REVERT: C 324 GLU cc_start: 0.6758 (tp30) cc_final: 0.6532 (tp30) REVERT: C 503 PHE cc_start: 0.4778 (m-10) cc_final: 0.4240 (m-80) REVERT: A 111 HIS cc_start: 0.8172 (p-80) cc_final: 0.7635 (m-70) REVERT: A 489 ILE cc_start: 0.9344 (pt) cc_final: 0.9062 (pt) REVERT: D 14 ASP cc_start: 0.7969 (p0) cc_final: 0.7101 (p0) REVERT: D 193 ARG cc_start: 0.6354 (tpt170) cc_final: 0.5866 (tpt170) REVERT: D 215 CYS cc_start: 0.6942 (m) cc_final: 0.6726 (m) REVERT: D 268 LEU cc_start: 0.8669 (mm) cc_final: 0.8403 (pp) REVERT: D 277 MET cc_start: 0.8256 (tmm) cc_final: 0.8038 (ppp) REVERT: D 336 MET cc_start: 0.7330 (mmp) cc_final: 0.6644 (mmp) REVERT: I 280 TYR cc_start: 0.7840 (m-10) cc_final: 0.7514 (m-10) REVERT: I 304 PHE cc_start: 0.8492 (t80) cc_final: 0.8110 (t80) REVERT: J 262 GLN cc_start: 0.8685 (mp10) cc_final: 0.8314 (mp10) REVERT: J 294 TRP cc_start: 0.5750 (p-90) cc_final: 0.5141 (p-90) REVERT: J 336 MET cc_start: 0.7383 (pmm) cc_final: 0.7025 (pmm) REVERT: J 411 PHE cc_start: 0.7901 (p90) cc_final: 0.7683 (p90) REVERT: N 260 GLU cc_start: 0.6309 (pm20) cc_final: 0.5948 (mt-10) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.2011 time to fit residues: 124.2571 Evaluate side-chains 266 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 207 HIS ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 GLN A 430 GLN D 357 GLN ** B 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 188 HIS I 61 GLN I 90 ASN ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS M 69 ASN M 90 ASN ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 374 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.101309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.083575 restraints weight = 125818.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.085232 restraints weight = 86554.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.085821 restraints weight = 64106.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.086321 restraints weight = 54640.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.086418 restraints weight = 50131.205| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3441 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3441 r_free = 0.3441 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3441 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 33108 Z= 0.254 Angle : 0.725 10.314 45425 Z= 0.393 Chirality : 0.049 0.298 4909 Planarity : 0.005 0.060 5180 Dihedral : 17.219 171.548 5785 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 0.16 % Allowed : 7.59 % Favored : 92.25 % 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: -2.10 (0.14), residues: 3457 helix: 0.31 (0.16), residues: 1028 sheet: -1.68 (0.21), residues: 622 loop : -2.38 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 19 TYR 0.030 0.002 TYR B 213 PHE 0.025 0.002 PHE C 503 TRP 0.016 0.002 TRP D 175 HIS 0.008 0.002 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.25 (33108) covalent geometry : angle 0.72545 / 0.39 (45425) hydrogen bonds : bond 0.05322 / 3.45 ( 1033) hydrogen bonds : angle 5.13648 / 3.51 ( 2791) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 325 time to evaluate : 1.187 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: C 36 ILE cc_start: 0.8571 (mm) cc_final: 0.8158 (tp) REVERT: C 303 MET cc_start: 0.8212 (ptt) cc_final: 0.7970 (ptm) REVERT: A 302 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7399 (pm20) REVERT: A 430 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8132 (tm-30) REVERT: D 133 ASP cc_start: 0.8988 (p0) cc_final: 0.8753 (p0) REVERT: D 277 MET cc_start: 0.8213 (tmm) cc_final: 0.7977 (tmm) REVERT: D 323 ILE cc_start: 0.6499 (pt) cc_final: 0.6111 (pt) REVERT: D 328 LYS cc_start: 0.7886 (mmtp) cc_final: 0.7661 (mmmm) REVERT: D 336 MET cc_start: 0.6828 (mmp) cc_final: 0.6610 (mmp) REVERT: B 151 ASN cc_start: 0.7724 (p0) cc_final: 0.7512 (p0) REVERT: B 393 LEU cc_start: 0.8845 (mm) cc_final: 0.8643 (mm) REVERT: J 262 GLN cc_start: 0.8726 (mp10) cc_final: 0.8389 (mp10) REVERT: J 294 TRP cc_start: 0.6076 (p-90) cc_final: 0.5207 (p-90) REVERT: J 336 MET cc_start: 0.7540 (pmm) cc_final: 0.7228 (pmm) REVERT: M 370 TRP cc_start: 0.6585 (t-100) cc_final: 0.6002 (t-100) outliers start: 5 outliers final: 1 residues processed: 330 average time/residue: 0.1957 time to fit residues: 106.7512 Evaluate side-chains 248 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 245 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 255 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 346 optimal weight: 30.0000 chunk 1 optimal weight: 0.6980 chunk 324 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 44 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 227 optimal weight: 6.9990 chunk 198 optimal weight: 1.9990 chunk 203 optimal weight: 9.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN C 360 HIS C 374 ASN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 GLN A 341 GLN D 358 HIS D 370 ASN B 109 ASN ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS M 69 ASN M 251 HIS ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.102701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.084757 restraints weight = 126372.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.086519 restraints weight = 87631.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.087063 restraints weight = 63603.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.087410 restraints weight = 55985.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.087662 restraints weight = 51593.932| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 33108 Z= 0.185 Angle : 0.666 10.985 45425 Z= 0.362 Chirality : 0.048 0.265 4909 Planarity : 0.005 0.141 5180 Dihedral : 17.205 171.413 5785 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 0.06 % Allowed : 5.37 % Favored : 94.56 % 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: -2.12 (0.14), residues: 3457 helix: 0.26 (0.16), residues: 1033 sheet: -1.62 (0.21), residues: 599 loop : -2.41 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 362 TYR 0.032 0.002 TYR M 346 PHE 0.027 0.002 PHE A 503 TRP 0.014 0.001 TRP D 319 HIS 0.011 0.001 HIS D 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.19 (33108) covalent geometry : angle 0.66551 / 0.36 (45425) hydrogen bonds : bond 0.04827 / 3.13 ( 1033) hydrogen bonds : angle 4.97816 / 3.42 ( 2791) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 333 time to evaluate : 1.456 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: C 36 ILE cc_start: 0.8438 (mm) cc_final: 0.8083 (tp) REVERT: C 503 PHE cc_start: 0.5528 (m-80) cc_final: 0.4789 (m-80) REVERT: A 341 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7366 (tp40) REVERT: D 13 GLU cc_start: 0.8470 (pp20) cc_final: 0.8170 (pp20) REVERT: D 14 ASP cc_start: 0.7991 (p0) cc_final: 0.7741 (p0) REVERT: D 133 ASP cc_start: 0.9026 (p0) cc_final: 0.8820 (p0) REVERT: D 277 MET cc_start: 0.8208 (tmm) cc_final: 0.7964 (tmm) REVERT: D 401 ILE cc_start: 0.8738 (mt) cc_final: 0.8487 (mm) REVERT: B 192 TRP cc_start: 0.7322 (p-90) cc_final: 0.6822 (p90) REVERT: B 393 LEU cc_start: 0.8803 (mm) cc_final: 0.8583 (mm) REVERT: I 304 PHE cc_start: 0.8699 (t80) cc_final: 0.8369 (t80) REVERT: J 262 GLN cc_start: 0.8688 (mp10) cc_final: 0.8370 (mp10) REVERT: J 294 TRP cc_start: 0.6082 (p-90) cc_final: 0.5052 (p-90) REVERT: J 336 MET cc_start: 0.7438 (pmm) cc_final: 0.7136 (pmm) REVERT: M 370 TRP cc_start: 0.6643 (t-100) cc_final: 0.6065 (t-100) outliers start: 2 outliers final: 0 residues processed: 335 average time/residue: 0.1958 time to fit residues: 108.6952 Evaluate side-chains 248 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 206 optimal weight: 9.9990 chunk 258 optimal weight: 10.0000 chunk 246 optimal weight: 0.9980 chunk 15 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 245 optimal weight: 0.5980 chunk 205 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 201 optimal weight: 0.9990 chunk 139 optimal weight: 0.5980 chunk 222 optimal weight: 6.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 ASN ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS M 69 ASN M 251 HIS ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.104822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.086094 restraints weight = 121816.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.087858 restraints weight = 77013.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.089028 restraints weight = 56732.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.089805 restraints weight = 46207.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.090333 restraints weight = 40348.154| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 33108 Z= 0.126 Angle : 0.619 10.986 45425 Z= 0.335 Chirality : 0.046 0.255 4909 Planarity : 0.004 0.074 5180 Dihedral : 17.132 171.316 5785 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 0.03 % Allowed : 4.50 % Favored : 95.46 % 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: -1.90 (0.14), residues: 3457 helix: 0.43 (0.16), residues: 1025 sheet: -1.40 (0.21), residues: 599 loop : -2.29 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 193 TYR 0.018 0.001 TYR B 213 PHE 0.021 0.001 PHE C 425 TRP 0.022 0.001 TRP B 192 HIS 0.007 0.001 HIS J 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (33108) covalent geometry : angle 0.61852 / 0.33 (45425) hydrogen bonds : bond 0.04074 / 2.65 ( 1033) hydrogen bonds : angle 4.70542 / 3.23 ( 2791) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 359 time to evaluate : 1.131 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: C 36 ILE cc_start: 0.8312 (mm) cc_final: 0.8019 (tp) REVERT: C 303 MET cc_start: 0.7738 (ptm) cc_final: 0.7504 (ptm) REVERT: C 406 MET cc_start: 0.8096 (tmm) cc_final: 0.7783 (tmm) REVERT: C 503 PHE cc_start: 0.5299 (m-80) cc_final: 0.3909 (m-80) REVERT: A 111 HIS cc_start: 0.7982 (p-80) cc_final: 0.7582 (m-70) REVERT: D 99 ILE cc_start: 0.8692 (pt) cc_final: 0.8187 (mt) REVERT: D 277 MET cc_start: 0.8197 (tmm) cc_final: 0.7839 (tmm) REVERT: D 323 ILE cc_start: 0.6495 (pt) cc_final: 0.6056 (pt) REVERT: D 401 ILE cc_start: 0.8713 (mt) cc_final: 0.8467 (mm) REVERT: B 393 LEU cc_start: 0.8820 (mm) cc_final: 0.8498 (mm) REVERT: I 309 ASP cc_start: 0.7767 (t0) cc_final: 0.7519 (t0) REVERT: J 262 GLN cc_start: 0.8594 (mp10) cc_final: 0.8349 (mp10) REVERT: J 294 TRP cc_start: 0.5897 (p-90) cc_final: 0.4980 (p-90) REVERT: J 336 MET cc_start: 0.7332 (pmm) cc_final: 0.7029 (pmm) REVERT: M 362 ARG cc_start: 0.7180 (ttp80) cc_final: 0.6720 (ttp80) outliers start: 1 outliers final: 0 residues processed: 360 average time/residue: 0.1921 time to fit residues: 113.5265 Evaluate side-chains 259 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 104 optimal weight: 7.9990 chunk 276 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 350 optimal weight: 30.0000 chunk 215 optimal weight: 5.9990 chunk 320 optimal weight: 20.0000 chunk 9 optimal weight: 0.4980 chunk 190 optimal weight: 9.9990 chunk 246 optimal weight: 0.0970 chunk 339 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 340 HIS ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS M 69 ASN M 251 HIS ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.104823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.085933 restraints weight = 124426.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.087703 restraints weight = 79725.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.088860 restraints weight = 59035.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.089637 restraints weight = 48396.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.090161 restraints weight = 42297.663| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7541 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33108 Z= 0.132 Angle : 0.614 11.236 45425 Z= 0.332 Chirality : 0.046 0.254 4909 Planarity : 0.004 0.121 5180 Dihedral : 17.131 171.781 5785 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % 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: -1.89 (0.14), residues: 3457 helix: 0.48 (0.16), residues: 1016 sheet: -1.43 (0.21), residues: 611 loop : -2.28 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 19 TYR 0.017 0.001 TYR C 411 PHE 0.018 0.001 PHE A 403 TRP 0.015 0.001 TRP B 192 HIS 0.014 0.001 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (33108) covalent geometry : angle 0.61360 / 0.33 (45425) hydrogen bonds : bond 0.04036 / 2.62 ( 1033) hydrogen bonds : angle 4.65485 / 3.19 ( 2791) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 351 time to evaluate : 1.188 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: C 36 ILE cc_start: 0.8301 (mm) cc_final: 0.7969 (tp) REVERT: A 111 HIS cc_start: 0.8026 (p-80) cc_final: 0.7570 (m-70) REVERT: D 74 VAL cc_start: 0.8519 (m) cc_final: 0.8177 (p) REVERT: D 99 ILE cc_start: 0.8726 (pt) cc_final: 0.8290 (mt) REVERT: D 100 ASP cc_start: 0.7945 (t0) cc_final: 0.7519 (t0) REVERT: D 133 ASP cc_start: 0.9033 (p0) cc_final: 0.8805 (p0) REVERT: D 277 MET cc_start: 0.8208 (tmm) cc_final: 0.7723 (ppp) REVERT: D 323 ILE cc_start: 0.6456 (pt) cc_final: 0.6001 (pt) REVERT: D 401 ILE cc_start: 0.8712 (mt) cc_final: 0.8461 (mm) REVERT: B 393 LEU cc_start: 0.8829 (mm) cc_final: 0.8516 (mm) REVERT: I 309 ASP cc_start: 0.7779 (t0) cc_final: 0.7551 (t0) REVERT: J 251 TYR cc_start: 0.6299 (t80) cc_final: 0.5857 (t80) REVERT: J 294 TRP cc_start: 0.6095 (p-90) cc_final: 0.5190 (p-90) REVERT: J 336 MET cc_start: 0.7515 (pmm) cc_final: 0.7183 (pmm) REVERT: M 362 ARG cc_start: 0.7241 (ttp80) cc_final: 0.6793 (ttp80) outliers start: 0 outliers final: 0 residues processed: 351 average time/residue: 0.1912 time to fit residues: 111.7425 Evaluate side-chains 263 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 99 optimal weight: 0.0980 chunk 267 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 288 optimal weight: 0.9980 chunk 210 optimal weight: 3.9990 chunk 230 optimal weight: 8.9990 chunk 227 optimal weight: 0.0010 chunk 116 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN A 35 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS M 69 ASN M 251 HIS ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.105062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.086245 restraints weight = 121937.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.088015 restraints weight = 77232.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.089183 restraints weight = 56834.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.089975 restraints weight = 46280.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.090509 restraints weight = 40280.321| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 33108 Z= 0.125 Angle : 0.609 11.611 45425 Z= 0.328 Chirality : 0.046 0.256 4909 Planarity : 0.004 0.062 5180 Dihedral : 17.099 171.745 5785 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.83 (0.14), residues: 3457 helix: 0.54 (0.16), residues: 1015 sheet: -1.38 (0.21), residues: 611 loop : -2.26 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.033 0.001 TYR B 213 PHE 0.020 0.001 PHE C 75 TRP 0.043 0.001 TRP N 46 HIS 0.008 0.001 HIS J 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (33108) covalent geometry : angle 0.60915 / 0.33 (45425) hydrogen bonds : bond 0.03839 / 2.49 ( 1033) hydrogen bonds : angle 4.58709 / 3.16 ( 2791) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 358 time to evaluate : 1.274 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: C 1 MET cc_start: 0.2686 (tpt) cc_final: 0.1780 (tpt) REVERT: C 36 ILE cc_start: 0.8310 (mm) cc_final: 0.8063 (mm) REVERT: A 111 HIS cc_start: 0.8018 (p-80) cc_final: 0.7566 (m-70) REVERT: A 353 TYR cc_start: 0.6940 (m-80) cc_final: 0.6700 (m-80) REVERT: A 411 TYR cc_start: 0.7949 (t80) cc_final: 0.7701 (t80) REVERT: D 74 VAL cc_start: 0.8624 (m) cc_final: 0.8273 (p) REVERT: D 99 ILE cc_start: 0.8716 (pt) cc_final: 0.8261 (mt) REVERT: D 100 ASP cc_start: 0.7924 (t0) cc_final: 0.7410 (t0) REVERT: D 133 ASP cc_start: 0.9017 (p0) cc_final: 0.8807 (p0) REVERT: D 277 MET cc_start: 0.8235 (tmm) cc_final: 0.7971 (ppp) REVERT: D 401 ILE cc_start: 0.8696 (mt) cc_final: 0.8453 (mm) REVERT: B 151 ASN cc_start: 0.7758 (p0) cc_final: 0.7547 (p0) REVERT: B 393 LEU cc_start: 0.8814 (mm) cc_final: 0.8495 (mm) REVERT: J 251 TYR cc_start: 0.6258 (t80) cc_final: 0.5878 (t80) REVERT: J 262 GLN cc_start: 0.8627 (mp10) cc_final: 0.8409 (mp10) REVERT: J 294 TRP cc_start: 0.6144 (p-90) cc_final: 0.5207 (p-90) REVERT: J 336 MET cc_start: 0.7461 (pmm) cc_final: 0.7109 (pmm) REVERT: M 362 ARG cc_start: 0.7170 (ttp80) cc_final: 0.6698 (ttp80) outliers start: 2 outliers final: 0 residues processed: 359 average time/residue: 0.1972 time to fit residues: 117.1863 Evaluate side-chains 256 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 169 optimal weight: 6.9990 chunk 348 optimal weight: 9.9990 chunk 264 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 254 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 209 optimal weight: 0.2980 chunk 237 optimal weight: 9.9990 chunk 224 optimal weight: 8.9990 chunk 236 optimal weight: 7.9990 chunk 314 optimal weight: 5.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 66 ASN ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN C 360 HIS ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS D 370 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS M 69 ASN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS M 295 GLN ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.101495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.082977 restraints weight = 124177.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.084619 restraints weight = 80339.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.085717 restraints weight = 59910.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.086447 restraints weight = 49065.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.086929 restraints weight = 43033.579| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3448 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3448 r_free = 0.3448 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3448 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 33108 Z= 0.234 Angle : 0.727 10.545 45425 Z= 0.390 Chirality : 0.049 0.262 4909 Planarity : 0.005 0.077 5180 Dihedral : 17.276 172.190 5785 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 0.03 % Allowed : 2.57 % Favored : 97.39 % 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: -2.17 (0.14), residues: 3457 helix: 0.26 (0.16), residues: 1021 sheet: -1.66 (0.21), residues: 589 loop : -2.44 (0.14), residues: 1847 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 19 TYR 0.027 0.002 TYR J 30 PHE 0.025 0.002 PHE D 60 TRP 0.040 0.002 TRP D 33 HIS 0.009 0.002 HIS J 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.23 (33108) covalent geometry : angle 0.72675 / 0.39 (45425) hydrogen bonds : bond 0.04930 / 3.20 ( 1033) hydrogen bonds : angle 4.94393 / 3.41 ( 2791) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 325 time to evaluate : 1.351 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: C 1 MET cc_start: 0.2924 (tpt) cc_final: 0.2300 (tpt) REVERT: C 36 ILE cc_start: 0.8547 (mm) cc_final: 0.8090 (tp) REVERT: C 95 GLU cc_start: 0.7450 (tp30) cc_final: 0.7196 (tp30) REVERT: A 353 TYR cc_start: 0.7199 (m-80) cc_final: 0.6916 (m-80) REVERT: D 188 HIS cc_start: 0.7380 (t70) cc_final: 0.7091 (t-170) REVERT: D 215 CYS cc_start: 0.6461 (m) cc_final: 0.6252 (m) REVERT: D 287 MET cc_start: 0.8234 (tpt) cc_final: 0.8033 (tpp) REVERT: D 323 ILE cc_start: 0.6549 (pt) cc_final: 0.6193 (pt) REVERT: D 401 ILE cc_start: 0.8747 (mt) cc_final: 0.8486 (mm) REVERT: B 151 ASN cc_start: 0.7791 (p0) cc_final: 0.7575 (p0) REVERT: J 251 TYR cc_start: 0.6308 (t80) cc_final: 0.5901 (t80) REVERT: J 262 GLN cc_start: 0.8650 (mp10) cc_final: 0.8427 (mp10) REVERT: J 294 TRP cc_start: 0.6420 (p-90) cc_final: 0.5197 (p-90) REVERT: J 336 MET cc_start: 0.7557 (pmm) cc_final: 0.7168 (pmm) outliers start: 1 outliers final: 0 residues processed: 325 average time/residue: 0.1899 time to fit residues: 103.6381 Evaluate side-chains 242 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 1.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 130 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 236 optimal weight: 0.2980 chunk 217 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 258 optimal weight: 10.0000 chunk 96 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 264 optimal weight: 0.0570 chunk 355 optimal weight: 10.0000 chunk 235 optimal weight: 5.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN C 360 HIS ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.104713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.085891 restraints weight = 120601.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.087601 restraints weight = 77014.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.088770 restraints weight = 57116.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.089537 restraints weight = 46636.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.090059 restraints weight = 40736.928| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3513 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3513 r_free = 0.3513 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3513 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 33108 Z= 0.128 Angle : 0.640 11.904 45425 Z= 0.341 Chirality : 0.046 0.258 4909 Planarity : 0.004 0.080 5180 Dihedral : 17.160 171.168 5785 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.67 % Favored : 92.33 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % 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: -1.87 (0.14), residues: 3457 helix: 0.53 (0.16), residues: 1010 sheet: -1.35 (0.22), residues: 572 loop : -2.30 (0.14), residues: 1875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG D 189 TYR 0.028 0.001 TYR B 213 PHE 0.028 0.001 PHE I 403 TRP 0.031 0.001 TRP D 33 HIS 0.008 0.001 HIS J 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (33108) covalent geometry : angle 0.63977 / 0.34 (45425) hydrogen bonds : bond 0.03903 / 2.54 ( 1033) hydrogen bonds : angle 4.60550 / 3.16 ( 2791) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 1.182 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: C 95 GLU cc_start: 0.7299 (tp30) cc_final: 0.6992 (tp30) REVERT: C 476 GLU cc_start: 0.8783 (pm20) cc_final: 0.7996 (pm20) REVERT: A 111 HIS cc_start: 0.7947 (p-80) cc_final: 0.7426 (m-70) REVERT: A 353 TYR cc_start: 0.6979 (m-80) cc_final: 0.6696 (m-80) REVERT: A 411 TYR cc_start: 0.7891 (t80) cc_final: 0.7658 (t80) REVERT: D 323 ILE cc_start: 0.6347 (pt) cc_final: 0.5930 (pt) REVERT: D 401 ILE cc_start: 0.8706 (mt) cc_final: 0.8454 (mm) REVERT: B 151 ASN cc_start: 0.7682 (p0) cc_final: 0.7436 (p0) REVERT: I 243 ARG cc_start: 0.6083 (mtp180) cc_final: 0.5529 (mtp180) REVERT: J 77 GLU cc_start: 0.7491 (tp30) cc_final: 0.7153 (tp30) REVERT: J 251 TYR cc_start: 0.6233 (t80) cc_final: 0.5969 (t80) REVERT: J 294 TRP cc_start: 0.6468 (p-90) cc_final: 0.5302 (p-90) REVERT: J 336 MET cc_start: 0.7399 (pmm) cc_final: 0.7036 (pmm) REVERT: M 362 ARG cc_start: 0.7138 (ttp80) cc_final: 0.6548 (ttp80) outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.1917 time to fit residues: 110.6981 Evaluate side-chains 254 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 107 optimal weight: 8.9990 chunk 282 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 317 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 236 optimal weight: 8.9990 chunk 300 optimal weight: 0.8980 chunk 328 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 232 optimal weight: 8.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS D 370 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.104027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.085191 restraints weight = 122829.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.086920 restraints weight = 78379.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.088060 restraints weight = 58024.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.088852 restraints weight = 47471.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.089360 restraints weight = 41360.132| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3493 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3493 r_free = 0.3493 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3493 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33108 Z= 0.145 Angle : 0.644 11.975 45425 Z= 0.345 Chirality : 0.046 0.255 4909 Planarity : 0.004 0.084 5180 Dihedral : 17.187 171.507 5785 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 0.06 % Allowed : 0.90 % Favored : 99.04 % 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: -1.91 (0.14), residues: 3457 helix: 0.45 (0.16), residues: 1018 sheet: -1.30 (0.22), residues: 558 loop : -2.32 (0.14), residues: 1881 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 257 TYR 0.026 0.001 TYR B 213 PHE 0.026 0.001 PHE I 403 TRP 0.023 0.001 TRP B 192 HIS 0.010 0.001 HIS J 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (33108) covalent geometry : angle 0.64423 / 0.34 (45425) hydrogen bonds : bond 0.04014 / 2.61 ( 1033) hydrogen bonds : angle 4.67076 / 3.23 ( 2791) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 339 time to evaluate : 1.186 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: C 95 GLU cc_start: 0.7359 (tp30) cc_final: 0.7153 (tp30) REVERT: A 111 HIS cc_start: 0.7985 (p-80) cc_final: 0.7409 (m-70) REVERT: A 411 TYR cc_start: 0.7925 (t80) cc_final: 0.7675 (t80) REVERT: D 323 ILE cc_start: 0.6403 (pt) cc_final: 0.5982 (pt) REVERT: D 328 LYS cc_start: 0.7785 (mmtp) cc_final: 0.7503 (mmmm) REVERT: D 401 ILE cc_start: 0.8718 (mt) cc_final: 0.8479 (mm) REVERT: B 151 ASN cc_start: 0.7604 (p0) cc_final: 0.7345 (p0) REVERT: I 243 ARG cc_start: 0.6098 (mtp180) cc_final: 0.5543 (mtp180) REVERT: J 77 GLU cc_start: 0.7543 (tp30) cc_final: 0.7199 (tp30) REVERT: J 251 TYR cc_start: 0.6321 (t80) cc_final: 0.6115 (t80) REVERT: J 262 GLN cc_start: 0.8653 (mp10) cc_final: 0.8300 (mp10) REVERT: J 294 TRP cc_start: 0.6548 (p-90) cc_final: 0.5342 (p-90) REVERT: J 336 MET cc_start: 0.7508 (pmm) cc_final: 0.7114 (pmm) REVERT: J 382 ARG cc_start: 0.5160 (mmt180) cc_final: 0.4550 (mmt-90) REVERT: M 362 ARG cc_start: 0.7236 (ttp80) cc_final: 0.6643 (ttp80) outliers start: 2 outliers final: 0 residues processed: 339 average time/residue: 0.1891 time to fit residues: 107.5642 Evaluate side-chains 261 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 166 optimal weight: 5.9990 chunk 306 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 345 optimal weight: 20.0000 chunk 83 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 273 optimal weight: 0.0980 chunk 64 optimal weight: 1.9990 chunk 170 optimal weight: 0.0050 chunk 90 optimal weight: 5.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN A 35 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN ** M 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.105411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.086546 restraints weight = 120603.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.088354 restraints weight = 75856.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.089586 restraints weight = 55526.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.090384 restraints weight = 44762.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.090904 restraints weight = 38846.879| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3528 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3528 r_free = 0.3528 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3528 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 33108 Z= 0.123 Angle : 0.638 12.438 45425 Z= 0.338 Chirality : 0.046 0.258 4909 Planarity : 0.004 0.071 5180 Dihedral : 17.141 171.300 5785 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.67 % Favored : 92.31 % Rotamer: Outliers : 0.06 % Allowed : 0.45 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.81 (0.14), residues: 3457 helix: 0.51 (0.16), residues: 1011 sheet: -1.25 (0.22), residues: 580 loop : -2.25 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 257 TYR 0.028 0.001 TYR B 213 PHE 0.030 0.001 PHE J 93 TRP 0.021 0.001 TRP B 192 HIS 0.010 0.001 HIS J 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (33108) covalent geometry : angle 0.63760 / 0.34 (45425) hydrogen bonds : bond 0.03678 / 2.39 ( 1033) hydrogen bonds : angle 4.54463 / 3.14 ( 2791) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 348 time to evaluate : 1.191 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: C 7 ILE cc_start: 0.8047 (mm) cc_final: 0.7758 (mm) REVERT: C 95 GLU cc_start: 0.7324 (tp30) cc_final: 0.7088 (tp30) REVERT: C 117 LEU cc_start: 0.8530 (mm) cc_final: 0.7742 (tp) REVERT: C 476 GLU cc_start: 0.8525 (pm20) cc_final: 0.8019 (pm20) REVERT: A 111 HIS cc_start: 0.8052 (p-80) cc_final: 0.7457 (m-70) REVERT: D 74 VAL cc_start: 0.8399 (m) cc_final: 0.8053 (p) REVERT: D 323 ILE cc_start: 0.6429 (pt) cc_final: 0.6009 (pt) REVERT: D 328 LYS cc_start: 0.7835 (mmtp) cc_final: 0.7576 (mmmm) REVERT: D 401 ILE cc_start: 0.8662 (mt) cc_final: 0.8408 (mm) REVERT: B 151 ASN cc_start: 0.7527 (p0) cc_final: 0.7266 (p0) REVERT: B 271 LYS cc_start: 0.7352 (tmmt) cc_final: 0.7073 (tmtt) REVERT: I 243 ARG cc_start: 0.6055 (mtp180) cc_final: 0.5504 (mtp180) REVERT: J 77 GLU cc_start: 0.7474 (tp30) cc_final: 0.7143 (tp30) REVERT: J 262 GLN cc_start: 0.8618 (mp10) cc_final: 0.8261 (mp10) REVERT: J 294 TRP cc_start: 0.6531 (p-90) cc_final: 0.5284 (p-90) REVERT: J 336 MET cc_start: 0.7462 (pmm) cc_final: 0.7101 (pmm) REVERT: J 382 ARG cc_start: 0.4951 (mmt180) cc_final: 0.4384 (mmt-90) REVERT: M 362 ARG cc_start: 0.7060 (ttp80) cc_final: 0.6386 (tmm160) outliers start: 2 outliers final: 0 residues processed: 348 average time/residue: 0.1894 time to fit residues: 110.3224 Evaluate side-chains 267 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 137 optimal weight: 0.6980 chunk 253 optimal weight: 1.9990 chunk 245 optimal weight: 2.9990 chunk 344 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 107 optimal weight: 4.9990 chunk 180 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 278 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 5.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 302 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 430 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS D 370 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN ** M 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.104159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.085436 restraints weight = 121228.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.087195 restraints weight = 76725.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.088366 restraints weight = 56434.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.089160 restraints weight = 45796.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.089672 restraints weight = 39806.530| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33108 Z= 0.144 Angle : 0.643 12.217 45425 Z= 0.343 Chirality : 0.046 0.256 4909 Planarity : 0.004 0.057 5180 Dihedral : 17.172 171.400 5785 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.91 % Favored : 91.06 % Rotamer: Outliers : 0.03 % Allowed : 0.48 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.86 (0.14), residues: 3457 helix: 0.46 (0.16), residues: 1018 sheet: -1.33 (0.22), residues: 578 loop : -2.26 (0.14), residues: 1861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG D 201 TYR 0.025 0.001 TYR B 213 PHE 0.034 0.001 PHE B 273 TRP 0.022 0.001 TRP B 192 HIS 0.011 0.001 HIS J 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (33108) covalent geometry : angle 0.64289 / 0.34 (45425) hydrogen bonds : bond 0.03852 / 2.49 ( 1033) hydrogen bonds : angle 4.58472 / 3.16 ( 2791) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5480.91 seconds wall clock time: 96 minutes 13.14 seconds (5773.14 seconds total)