Starting phenix.real_space_refine on Mon Jul 6 01:29:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jay_36138/07_2026/8jay_36138.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jay_36138/07_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_36138/07_2026/8jay_36138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jay_36138/07_2026/8jay_36138.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jay_36138/07_2026/8jay_36138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jay_36138/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.69, 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: 2.75 Conformation dependent library (CDL) restraints added in 1.3 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: 2.79 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: 5.86 Time building geometry restraints manager: 3.67 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: 44841 2.48 - 4.97: 518 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: 6.680 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: 0.030 Extract box with map and model: 0.550 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 28.860 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.360 ------------------------------------------------------------------------------- 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 : 0.682 12.423 45425 Z= 0.454 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 0.68249 / 0.45 (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 : 1.213 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: C 36 ILE cc_start: 0.8370 (mm) cc_final: 0.8153 (tp) REVERT: C 324 GLU cc_start: 0.6758 (tp30) cc_final: 0.6533 (tp30) REVERT: C 503 PHE cc_start: 0.4778 (m-10) cc_final: 0.4241 (m-80) REVERT: A 111 HIS cc_start: 0.8172 (p-80) cc_final: 0.7639 (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: 0.7100 (p0) REVERT: D 193 ARG cc_start: 0.6354 (tpt170) cc_final: 0.5867 (tpt170) REVERT: D 215 CYS cc_start: 0.6942 (m) cc_final: 0.6728 (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: 0.8039 (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: 0.5140 (p-90) REVERT: J 336 MET cc_start: 0.7383 (pmm) cc_final: 0.7026 (pmm) REVERT: J 411 PHE cc_start: 0.7901 (p90) cc_final: 0.7684 (p90) REVERT: N 260 GLU cc_start: 0.6309 (pm20) cc_final: 0.5938 (mt-10) REVERT: N 271 LYS cc_start: 0.8197 (mmtt) cc_final: 0.7826 (mmtt) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.1990 time to fit residues: 122.7460 Evaluate side-chains 265 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.107 ------------------------------------------------------------------------------- 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 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 HIS ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 374 ASN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 GLN A 302 GLN A 341 GLN A 430 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.100932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.082463 restraints weight = 126071.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.084096 restraints weight = 81472.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.085194 restraints weight = 60814.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.085939 restraints weight = 49866.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.086426 restraints weight = 43658.053| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- 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: 0.7654 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 33108 Z= 0.252 Angle : 0.732 10.395 45425 Z= 0.395 Chirality : 0.049 0.296 4909 Planarity : 0.005 0.063 5180 Dihedral : 17.282 171.685 5785 Min Nonbonded Distance : 1.684 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 0.19 % Allowed : 8.11 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.14), residues: 3457 helix: 0.26 (0.16), residues: 1028 sheet: -1.74 (0.21), residues: 607 loop : -2.40 (0.14), residues: 1822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 225 TYR 0.030 0.002 TYR B 213 PHE 0.027 0.002 PHE C 503 TRP 0.018 0.002 TRP D 175 HIS 0.010 0.002 HIS A 207 Details of bonding type rmsd/Z covalent geometry : bond 0.00547 / 0.25 (33108) covalent geometry : angle 0.73243 / 0.40 (45425) hydrogen bonds : bond 0.05446 / 3.55 ( 1033) hydrogen bonds : angle 5.14899 / 3.52 ( 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 331 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 325 time to evaluate : 1.147 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 303 MET cc_start: 0.8287 (ptt) cc_final: 0.8047 (ptm) REVERT: A 302 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7501 (pm20) REVERT: A 341 GLN cc_start: 0.8494 (OUTLIER) cc_final: 0.7306 (tp40) REVERT: A 430 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8163 (tm-30) REVERT: D 133 ASP cc_start: 0.9010 (p0) cc_final: 0.8770 (p0) REVERT: D 193 ARG cc_start: 0.6264 (tpt170) cc_final: 0.5653 (tpt170) REVERT: D 277 MET cc_start: 0.8220 (tmm) cc_final: 0.7975 (tmm) REVERT: D 323 ILE cc_start: 0.6579 (pt) cc_final: 0.6113 (pt) REVERT: D 328 LYS cc_start: 0.7856 (mmtp) cc_final: 0.7633 (mmmm) REVERT: D 336 MET cc_start: 0.6757 (mmp) cc_final: 0.6502 (mmp) REVERT: J 262 GLN cc_start: 0.8750 (mp10) cc_final: 0.8388 (mp10) REVERT: J 294 TRP cc_start: 0.6091 (p-90) cc_final: 0.5222 (p-90) REVERT: J 336 MET cc_start: 0.7551 (pmm) cc_final: 0.7243 (pmm) REVERT: N 271 LYS cc_start: 0.8103 (mmtt) cc_final: 0.7782 (mmtt) outliers start: 6 outliers final: 1 residues processed: 331 average time/residue: 0.1786 time to fit residues: 96.7496 Evaluate side-chains 248 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 244 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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: 4.9990 chunk 47 optimal weight: 2.9990 chunk 346 optimal weight: 30.0000 chunk 1 optimal weight: 0.8980 chunk 324 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 227 optimal weight: 0.6980 chunk 198 optimal weight: 0.0670 chunk 203 optimal weight: 10.0000 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 GLN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.104440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.085830 restraints weight = 123510.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.087561 restraints weight = 78811.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.088739 restraints weight = 58263.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.089510 restraints weight = 47408.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.089929 restraints weight = 41379.311| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 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 = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33108 Z= 0.136 Angle : 0.632 11.051 45425 Z= 0.343 Chirality : 0.046 0.258 4909 Planarity : 0.005 0.136 5180 Dihedral : 17.145 172.033 5785 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.03 % Allowed : 4.28 % Favored : 95.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.14), residues: 3457 helix: 0.35 (0.16), residues: 1034 sheet: -1.42 (0.21), residues: 604 loop : -2.34 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG N 209 TYR 0.028 0.001 TYR M 346 PHE 0.030 0.002 PHE A 503 TRP 0.020 0.001 TRP B 192 HIS 0.007 0.001 HIS D 9 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (33108) covalent geometry : angle 0.63250 / 0.34 (45425) hydrogen bonds : bond 0.04422 / 2.87 ( 1033) hydrogen bonds : angle 4.82042 / 3.30 ( 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 359 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 358 time to evaluate : 1.139 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: C 36 ILE cc_start: 0.8284 (mm) cc_final: 0.8004 (tp) REVERT: C 324 GLU cc_start: 0.6776 (tp30) cc_final: 0.6571 (tp30) REVERT: A 111 HIS cc_start: 0.8055 (p-80) cc_final: 0.7602 (m-70) REVERT: D 13 GLU cc_start: 0.8509 (pp20) cc_final: 0.8251 (pp20) REVERT: D 14 ASP cc_start: 0.8033 (p0) cc_final: 0.7601 (p0) REVERT: D 74 VAL cc_start: 0.8671 (m) cc_final: 0.8304 (p) REVERT: D 133 ASP cc_start: 0.9025 (p0) cc_final: 0.8825 (p0) REVERT: D 277 MET cc_start: 0.8174 (tmm) cc_final: 0.7929 (tmm) REVERT: D 401 ILE cc_start: 0.8719 (mt) cc_final: 0.8478 (mm) REVERT: B 192 TRP cc_start: 0.6952 (p-90) cc_final: 0.6383 (p90) REVERT: J 262 GLN cc_start: 0.8604 (mp10) cc_final: 0.8353 (mp10) REVERT: J 294 TRP cc_start: 0.6066 (p-90) cc_final: 0.5058 (p-90) REVERT: J 336 MET cc_start: 0.7366 (pmm) cc_final: 0.7057 (pmm) REVERT: N 271 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7759 (mmtt) outliers start: 1 outliers final: 1 residues processed: 359 average time/residue: 0.1895 time to fit residues: 111.8997 Evaluate side-chains 261 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 260 time to evaluate : 1.194 ------------------------------------------------------------------------------- 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: 10.0000 chunk 258 optimal weight: 10.0000 chunk 246 optimal weight: 0.6980 chunk 15 optimal weight: 0.0670 chunk 33 optimal weight: 6.9990 chunk 245 optimal weight: 0.0570 chunk 205 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 201 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 222 optimal weight: 7.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 207 HIS ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 357 GLN D 370 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.105137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.086652 restraints weight = 120829.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.088292 restraints weight = 79250.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.089407 restraints weight = 59636.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.090147 restraints weight = 49057.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.090641 restraints weight = 43070.988| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 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 = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1397 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= 0.124 Angle : 0.608 10.880 45425 Z= 0.329 Chirality : 0.046 0.249 4909 Planarity : 0.004 0.066 5180 Dihedral : 17.124 172.433 5785 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 0.03 % Allowed : 3.73 % Favored : 96.24 % 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: 0.51 (0.16), residues: 1016 sheet: -1.35 (0.21), residues: 599 loop : -2.25 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 364 TYR 0.017 0.001 TYR M 346 PHE 0.022 0.001 PHE A 313 TRP 0.031 0.001 TRP B 192 HIS 0.008 0.001 HIS D 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.12 (33108) covalent geometry : angle 0.60805 / 0.33 (45425) hydrogen bonds : bond 0.04005 / 2.61 ( 1033) hydrogen bonds : angle 4.67350 / 3.21 ( 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 361 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 360 time to evaluate : 1.177 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 36 ILE cc_start: 0.8219 (mm) cc_final: 0.7988 (tp) REVERT: C 406 MET cc_start: 0.7979 (tmm) cc_final: 0.7650 (tmm) REVERT: A 111 HIS cc_start: 0.8059 (p-80) cc_final: 0.7589 (m-70) REVERT: D 133 ASP cc_start: 0.8998 (p0) cc_final: 0.8788 (p0) REVERT: D 193 ARG cc_start: 0.5901 (tpt170) cc_final: 0.5254 (tpt170) REVERT: D 323 ILE cc_start: 0.6477 (pt) cc_final: 0.5997 (pt) REVERT: D 401 ILE cc_start: 0.8691 (mt) cc_final: 0.8452 (mm) REVERT: B 151 ASN cc_start: 0.7765 (p0) cc_final: 0.7563 (p0) REVERT: B 393 LEU cc_start: 0.8839 (mm) cc_final: 0.8536 (mm) REVERT: I 309 ASP cc_start: 0.7730 (t0) cc_final: 0.7504 (t0) REVERT: J 262 GLN cc_start: 0.8579 (mp10) cc_final: 0.8354 (mp10) REVERT: J 294 TRP cc_start: 0.5862 (p-90) cc_final: 0.4932 (p-90) REVERT: J 336 MET cc_start: 0.7318 (pmm) cc_final: 0.7003 (pmm) REVERT: J 411 PHE cc_start: 0.7962 (p90) cc_final: 0.7728 (p90) REVERT: N 271 LYS cc_start: 0.8120 (mmtt) cc_final: 0.7759 (mmtt) outliers start: 1 outliers final: 0 residues processed: 361 average time/residue: 0.1812 time to fit residues: 108.2825 Evaluate side-chains 260 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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: 9.9990 chunk 276 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 350 optimal weight: 30.0000 chunk 215 optimal weight: 9.9990 chunk 320 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 chunk 246 optimal weight: 0.4980 chunk 339 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 HIS ** 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 = 0.3784 r_free = 0.3784 target = 0.103270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.084653 restraints weight = 123675.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.086349 restraints weight = 78969.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.087489 restraints weight = 58642.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.088258 restraints weight = 47913.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.088771 restraints weight = 41729.969| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3488 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3488 r_free = 0.3488 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3488 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33108 Z= 0.169 Angle : 0.634 11.073 45425 Z= 0.344 Chirality : 0.046 0.242 4909 Planarity : 0.004 0.118 5180 Dihedral : 17.171 172.919 5785 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 0.06 % Allowed : 3.63 % Favored : 96.30 % 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: -1.98 (0.14), residues: 3457 helix: 0.41 (0.16), residues: 1024 sheet: -1.50 (0.21), residues: 600 loop : -2.34 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 362 TYR 0.020 0.002 TYR A 397 PHE 0.019 0.002 PHE A 403 TRP 0.025 0.001 TRP B 192 HIS 0.009 0.001 HIS D 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.17 (33108) covalent geometry : angle 0.63358 / 0.34 (45425) hydrogen bonds : bond 0.04356 / 2.82 ( 1033) hydrogen bonds : angle 4.73058 / 3.25 ( 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 343 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 341 time to evaluate : 1.252 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: 0.8393 (mm) cc_final: 0.8037 (tp) REVERT: D 74 VAL cc_start: 0.8589 (m) cc_final: 0.8230 (p) REVERT: D 133 ASP cc_start: 0.9003 (p0) cc_final: 0.8782 (p0) REVERT: D 193 ARG cc_start: 0.6031 (tpt170) cc_final: 0.5418 (tpt170) REVERT: D 323 ILE cc_start: 0.6575 (pt) cc_final: 0.6153 (pt) REVERT: D 401 ILE cc_start: 0.8732 (mt) cc_final: 0.8486 (mm) REVERT: B 151 ASN cc_start: 0.7784 (p0) cc_final: 0.7560 (p0) REVERT: B 393 LEU cc_start: 0.8736 (mm) cc_final: 0.8523 (mm) REVERT: I 309 ASP cc_start: 0.7856 (t0) cc_final: 0.7618 (t0) REVERT: J 262 GLN cc_start: 0.8668 (mp10) cc_final: 0.8351 (mp10) REVERT: J 294 TRP cc_start: 0.6131 (p-90) cc_final: 0.5176 (p-90) REVERT: J 336 MET cc_start: 0.7535 (pmm) cc_final: 0.7177 (pmm) REVERT: N 271 LYS cc_start: 0.8101 (mmtt) cc_final: 0.7759 (mmtt) outliers start: 2 outliers final: 1 residues processed: 342 average time/residue: 0.1773 time to fit residues: 100.7147 Evaluate side-chains 254 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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: 0.9980 chunk 267 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 chunk 288 optimal weight: 9.9990 chunk 210 optimal weight: 0.7980 chunk 230 optimal weight: 0.7980 chunk 227 optimal weight: 0.7980 chunk 116 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 340 HIS ** 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 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 = 0.3808 r_free = 0.3808 target = 0.104743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.085974 restraints weight = 121518.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.087704 restraints weight = 76974.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.088889 restraints weight = 56858.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.089671 restraints weight = 46300.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.090216 restraints weight = 40325.997| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 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 = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.1640 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= 0.129 Angle : 0.620 10.913 45425 Z= 0.334 Chirality : 0.046 0.234 4909 Planarity : 0.004 0.072 5180 Dihedral : 17.132 172.578 5785 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.06 % Allowed : 2.89 % Favored : 97.04 % 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: -1.86 (0.14), residues: 3457 helix: 0.51 (0.16), residues: 1016 sheet: -1.39 (0.21), residues: 604 loop : -2.26 (0.14), residues: 1837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 362 TYR 0.030 0.001 TYR B 213 PHE 0.019 0.001 PHE C 503 TRP 0.047 0.001 TRP B 192 HIS 0.008 0.001 HIS J 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 (33108) covalent geometry : angle 0.61997 / 0.33 (45425) hydrogen bonds : bond 0.03929 / 2.55 ( 1033) hydrogen bonds : angle 4.61380 / 3.17 ( 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 354 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 352 time to evaluate : 1.027 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: C 36 ILE cc_start: 0.8364 (mm) cc_final: 0.8103 (mm) REVERT: C 117 LEU cc_start: 0.8541 (mm) cc_final: 0.7715 (tp) REVERT: C 303 MET cc_start: 0.7861 (ptm) cc_final: 0.7590 (ptm) REVERT: A 111 HIS cc_start: 0.8002 (p-80) cc_final: 0.7445 (m-70) REVERT: A 353 TYR cc_start: 0.7008 (m-80) cc_final: 0.6747 (m-80) REVERT: D 74 VAL cc_start: 0.8652 (m) cc_final: 0.8309 (p) REVERT: D 99 ILE cc_start: 0.8762 (pt) cc_final: 0.8288 (mt) REVERT: D 100 ASP cc_start: 0.8052 (t0) cc_final: 0.7751 (t0) REVERT: D 130 ASP cc_start: 0.8636 (p0) cc_final: 0.8423 (p0) REVERT: D 133 ASP cc_start: 0.8973 (p0) cc_final: 0.8753 (p0) REVERT: D 277 MET cc_start: 0.8137 (ppp) cc_final: 0.7768 (ppp) REVERT: D 401 ILE cc_start: 0.8710 (mt) cc_final: 0.8449 (mm) REVERT: B 21 LEU cc_start: 0.9183 (mt) cc_final: 0.8974 (mm) REVERT: B 151 ASN cc_start: 0.7742 (p0) cc_final: 0.7517 (p0) REVERT: B 393 LEU cc_start: 0.8685 (mm) cc_final: 0.8348 (mm) REVERT: J 251 TYR cc_start: 0.6367 (t80) cc_final: 0.5952 (t80) REVERT: J 294 TRP cc_start: 0.6111 (p-90) cc_final: 0.5157 (p-90) REVERT: J 336 MET cc_start: 0.7419 (pmm) cc_final: 0.7066 (pmm) outliers start: 2 outliers final: 0 residues processed: 353 average time/residue: 0.1778 time to fit residues: 105.4485 Evaluate side-chains 257 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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: 0.9980 chunk 348 optimal weight: 10.0000 chunk 264 optimal weight: 3.9990 chunk 167 optimal weight: 6.9990 chunk 254 optimal weight: 0.0070 chunk 44 optimal weight: 10.0000 chunk 209 optimal weight: 0.0050 chunk 237 optimal weight: 10.0000 chunk 224 optimal weight: 7.9990 chunk 236 optimal weight: 7.9990 chunk 314 optimal weight: 3.9990 overall best weight: 1.8016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN 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 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 = 0.3796 r_free = 0.3796 target = 0.104020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.085265 restraints weight = 121529.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.086981 restraints weight = 77768.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.088110 restraints weight = 57741.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.088870 restraints weight = 47332.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.089383 restraints weight = 41380.481| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3501 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3501 r_free = 0.3501 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1744 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= 0.148 Angle : 0.634 11.883 45425 Z= 0.341 Chirality : 0.046 0.231 4909 Planarity : 0.004 0.076 5180 Dihedral : 17.149 172.703 5785 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 0.03 % Allowed : 2.09 % Favored : 97.88 % 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: -1.88 (0.14), residues: 3457 helix: 0.51 (0.16), residues: 1016 sheet: -1.38 (0.21), residues: 579 loop : -2.30 (0.14), residues: 1862 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 257 TYR 0.027 0.001 TYR B 213 PHE 0.031 0.002 PHE C 503 TRP 0.033 0.001 TRP B 192 HIS 0.009 0.001 HIS J 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (33108) covalent geometry : angle 0.63365 / 0.34 (45425) hydrogen bonds : bond 0.04052 / 2.62 ( 1033) hydrogen bonds : angle 4.63034 / 3.18 ( 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 348 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 347 time to evaluate : 1.236 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: C 1 MET cc_start: 0.2760 (tpt) cc_final: 0.1782 (tpt) REVERT: C 36 ILE cc_start: 0.8372 (mm) cc_final: 0.7950 (tp) REVERT: C 303 MET cc_start: 0.7934 (ptm) cc_final: 0.7587 (ptm) REVERT: A 111 HIS cc_start: 0.7971 (p-80) cc_final: 0.7415 (m-70) REVERT: A 225 ARG cc_start: 0.6129 (mtt90) cc_final: 0.5607 (mtt180) REVERT: A 353 TYR cc_start: 0.7025 (m-80) cc_final: 0.6774 (m-80) REVERT: D 99 ILE cc_start: 0.8756 (pt) cc_final: 0.8255 (mt) REVERT: D 133 ASP cc_start: 0.8953 (p0) cc_final: 0.8742 (p0) REVERT: D 277 MET cc_start: 0.8287 (ppp) cc_final: 0.7905 (ppp) REVERT: D 323 ILE cc_start: 0.6454 (pt) cc_final: 0.6062 (pt) REVERT: D 401 ILE cc_start: 0.8729 (mt) cc_final: 0.8466 (mm) REVERT: J 251 TYR cc_start: 0.6368 (t80) cc_final: 0.6066 (t80) REVERT: J 262 GLN cc_start: 0.8660 (mp10) cc_final: 0.8280 (mp10) REVERT: J 294 TRP cc_start: 0.6089 (p-90) cc_final: 0.5109 (p-90) REVERT: J 336 MET cc_start: 0.7461 (pmm) cc_final: 0.7093 (pmm) outliers start: 1 outliers final: 0 residues processed: 347 average time/residue: 0.1905 time to fit residues: 109.4640 Evaluate side-chains 252 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 252 time to evaluate : 1.213 ------------------------------------------------------------------------------- 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: 10.0000 chunk 42 optimal weight: 2.9990 chunk 236 optimal weight: 9.9990 chunk 217 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 258 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 90 optimal weight: 2.9990 chunk 264 optimal weight: 0.0270 chunk 355 optimal weight: 9.9990 chunk 235 optimal weight: 8.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.104001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.085278 restraints weight = 120799.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.087001 restraints weight = 77409.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.088130 restraints weight = 57351.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.088888 restraints weight = 46989.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.089415 restraints weight = 41096.329| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3500 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3500 r_free = 0.3500 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3500 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1830 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= 0.147 Angle : 0.641 11.921 45425 Z= 0.343 Chirality : 0.046 0.270 4909 Planarity : 0.004 0.080 5180 Dihedral : 17.150 172.542 5785 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.03 % Favored : 90.95 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.51 (0.16), residues: 1016 sheet: -1.36 (0.21), residues: 578 loop : -2.30 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 240 TYR 0.026 0.002 TYR B 213 PHE 0.029 0.001 PHE I 403 TRP 0.043 0.001 TRP B 192 HIS 0.009 0.001 HIS J 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (33108) covalent geometry : angle 0.64118 / 0.34 (45425) hydrogen bonds : bond 0.03990 / 2.58 ( 1033) hydrogen bonds : angle 4.61510 / 3.18 ( 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 343 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 1.137 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: 0.2743 (tpt) cc_final: 0.2055 (tpt) REVERT: C 303 MET cc_start: 0.7906 (ptm) cc_final: 0.7618 (ptm) REVERT: A 111 HIS cc_start: 0.7962 (p-80) cc_final: 0.7463 (m-70) REVERT: A 353 TYR cc_start: 0.7000 (m-80) cc_final: 0.6716 (m-80) REVERT: D 99 ILE cc_start: 0.8769 (pt) cc_final: 0.8257 (mt) REVERT: D 130 ASP cc_start: 0.8703 (p0) cc_final: 0.8467 (p0) REVERT: D 277 MET cc_start: 0.8289 (ppp) cc_final: 0.7923 (ppp) REVERT: D 323 ILE cc_start: 0.6395 (pt) cc_final: 0.6023 (pt) REVERT: D 401 ILE cc_start: 0.8730 (mt) cc_final: 0.8464 (mm) REVERT: B 151 ASN cc_start: 0.7737 (p0) cc_final: 0.7515 (p0) REVERT: I 243 ARG cc_start: 0.6096 (mtp180) cc_final: 0.5537 (mtp180) REVERT: J 77 GLU cc_start: 0.7518 (tp30) cc_final: 0.7160 (tp30) REVERT: J 251 TYR cc_start: 0.6334 (t80) cc_final: 0.6029 (t80) REVERT: J 294 TRP cc_start: 0.6132 (p-90) cc_final: 0.5141 (p-90) REVERT: J 336 MET cc_start: 0.7471 (pmm) cc_final: 0.7092 (pmm) outliers start: 0 outliers final: 0 residues processed: 343 average time/residue: 0.1801 time to fit residues: 101.5299 Evaluate side-chains 253 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.384 ------------------------------------------------------------------------------- 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: 9.9990 chunk 282 optimal weight: 10.0000 chunk 23 optimal weight: 0.0970 chunk 317 optimal weight: 5.9990 chunk 65 optimal weight: 0.0470 chunk 236 optimal weight: 7.9990 chunk 300 optimal weight: 4.9990 chunk 328 optimal weight: 3.9990 chunk 12 optimal weight: 0.0870 chunk 146 optimal weight: 0.6980 chunk 232 optimal weight: 9.9990 overall best weight: 0.9856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 295 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** ** M 329 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.105027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.086163 restraints weight = 120956.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.087932 restraints weight = 76943.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.089095 restraints weight = 56735.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.089897 restraints weight = 46209.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.090421 restraints weight = 40197.848| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3519 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3519 r_free = 0.3519 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 = 0.3519 r_free = 0.3519 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3519 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.1851 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= 0.127 Angle : 0.636 12.357 45425 Z= 0.340 Chirality : 0.046 0.248 4909 Planarity : 0.004 0.082 5180 Dihedral : 17.132 172.391 5785 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.33 % Favored : 91.64 % Rotamer: Outliers : 0.03 % Allowed : 0.61 % Favored : 99.36 % 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: -1.82 (0.14), residues: 3457 helix: 0.54 (0.16), residues: 1009 sheet: -1.32 (0.21), residues: 583 loop : -2.25 (0.14), residues: 1865 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 19 TYR 0.026 0.001 TYR B 213 PHE 0.026 0.001 PHE I 403 TRP 0.035 0.001 TRP B 192 HIS 0.010 0.001 HIS J 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.13 (33108) covalent geometry : angle 0.63641 / 0.34 (45425) hydrogen bonds : bond 0.03803 / 2.48 ( 1033) hydrogen bonds : angle 4.59191 / 3.18 ( 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 354 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 353 time to evaluate : 0.896 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 303 MET cc_start: 0.7831 (ptm) cc_final: 0.7518 (ptm) REVERT: A 111 HIS cc_start: 0.7985 (p-80) cc_final: 0.7540 (m-70) REVERT: A 353 TYR cc_start: 0.7112 (m-80) cc_final: 0.6857 (m-80) REVERT: D 193 ARG cc_start: 0.5398 (tpt170) cc_final: 0.4763 (tpt170) REVERT: D 215 CYS cc_start: 0.6886 (m) cc_final: 0.6677 (m) REVERT: D 277 MET cc_start: 0.8299 (ppp) cc_final: 0.7911 (ppp) REVERT: D 323 ILE cc_start: 0.6370 (pt) cc_final: 0.5981 (pt) REVERT: D 328 LYS cc_start: 0.7781 (mmtp) cc_final: 0.7515 (mmmm) REVERT: D 401 ILE cc_start: 0.8693 (mt) cc_final: 0.8445 (mm) REVERT: I 243 ARG cc_start: 0.6063 (mtp180) cc_final: 0.5514 (mtp180) REVERT: I 280 TYR cc_start: 0.8082 (m-80) cc_final: 0.7879 (m-10) REVERT: J 77 GLU cc_start: 0.7455 (tp30) cc_final: 0.7106 (tp30) REVERT: J 251 TYR cc_start: 0.6191 (t80) cc_final: 0.5962 (t80) REVERT: J 262 GLN cc_start: 0.8636 (mp10) cc_final: 0.8288 (mp10) REVERT: J 294 TRP cc_start: 0.6263 (p-90) cc_final: 0.5303 (p-90) REVERT: J 336 MET cc_start: 0.7465 (pmm) cc_final: 0.7067 (pmm) REVERT: J 382 ARG cc_start: 0.5529 (mmt180) cc_final: 0.5209 (tpt170) REVERT: M 1 MET cc_start: 0.5730 (pmm) cc_final: 0.5480 (pmm) outliers start: 1 outliers final: 0 residues processed: 353 average time/residue: 0.1767 time to fit residues: 103.8966 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 : 1.152 ------------------------------------------------------------------------------- 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: 4.9990 chunk 306 optimal weight: 0.0050 chunk 19 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 345 optimal weight: 20.0000 chunk 83 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 273 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 170 optimal weight: 0.7980 chunk 90 optimal weight: 6.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 236 GLN ** 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.105826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.086946 restraints weight = 121503.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.088719 restraints weight = 77003.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.089868 restraints weight = 56738.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.090675 restraints weight = 46380.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.091207 restraints weight = 40337.532| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 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: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1924 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 : 0.635 12.468 45425 Z= 0.338 Chirality : 0.046 0.246 4909 Planarity : 0.004 0.052 5180 Dihedral : 17.116 172.337 5785 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.93 % Favored : 92.05 % Rotamer: Outliers : 0.06 % Allowed : 0.39 % Favored : 99.55 % 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: -1.79 (0.14), residues: 3457 helix: 0.53 (0.16), residues: 1009 sheet: -1.20 (0.22), residues: 570 loop : -2.24 (0.14), residues: 1878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.028 0.001 TYR B 213 PHE 0.026 0.001 PHE I 403 TRP 0.041 0.001 TRP B 192 HIS 0.011 0.001 HIS J 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (33108) covalent geometry : angle 0.63489 / 0.34 (45425) hydrogen bonds : bond 0.03610 / 2.36 ( 1033) hydrogen bonds : angle 4.52933 / 3.13 ( 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 358 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 356 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 303 MET cc_start: 0.7775 (ptm) cc_final: 0.7495 (ptm) REVERT: C 476 GLU cc_start: 0.8608 (pm20) cc_final: 0.8097 (pm20) REVERT: A 111 HIS cc_start: 0.8116 (p-80) cc_final: 0.7581 (m-70) REVERT: A 353 TYR cc_start: 0.6999 (m-80) cc_final: 0.6747 (m-80) REVERT: D 74 VAL cc_start: 0.8461 (m) cc_final: 0.8153 (p) REVERT: D 277 MET cc_start: 0.8265 (ppp) cc_final: 0.7867 (ppp) REVERT: D 323 ILE cc_start: 0.6325 (pt) cc_final: 0.5929 (pt) REVERT: D 328 LYS cc_start: 0.7847 (mmtp) cc_final: 0.7588 (mmmm) REVERT: D 401 ILE cc_start: 0.8651 (mt) cc_final: 0.8310 (mm) REVERT: I 243 ARG cc_start: 0.5990 (mtp180) cc_final: 0.5443 (mtp180) REVERT: J 77 GLU cc_start: 0.7449 (tp30) cc_final: 0.7114 (tp30) REVERT: J 294 TRP cc_start: 0.6325 (p-90) cc_final: 0.5327 (p-90) REVERT: J 336 MET cc_start: 0.7509 (pmm) cc_final: 0.7143 (pmm) REVERT: J 382 ARG cc_start: 0.5515 (mmt180) cc_final: 0.5157 (tpt170) outliers start: 2 outliers final: 0 residues processed: 357 average time/residue: 0.1892 time to fit residues: 111.2585 Evaluate side-chains 264 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 1.152 ------------------------------------------------------------------------------- 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: 2.9990 chunk 253 optimal weight: 1.9990 chunk 245 optimal weight: 0.7980 chunk 344 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 107 optimal weight: 0.4980 chunk 180 optimal weight: 5.9990 chunk 203 optimal weight: 3.9990 chunk 278 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 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 J 370 ASN M 69 ASN ** M 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.104866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.086049 restraints weight = 121619.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.087788 restraints weight = 77285.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.088977 restraints weight = 57127.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.089763 restraints weight = 46464.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.090302 restraints weight = 40401.361| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3516 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3516 r_free = 0.3516 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3516 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7534 moved from start: 0.1962 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= 0.135 Angle : 0.633 12.512 45425 Z= 0.337 Chirality : 0.046 0.235 4909 Planarity : 0.004 0.050 5180 Dihedral : 17.137 172.424 5785 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.19 % Favored : 91.78 % Rotamer: Outliers : 0.03 % Allowed : 0.42 % Favored : 99.55 % 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: 1016 sheet: -1.28 (0.21), residues: 581 loop : -2.25 (0.14), residues: 1860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 19 TYR 0.025 0.001 TYR B 213 PHE 0.027 0.001 PHE B 273 TRP 0.036 0.001 TRP B 192 HIS 0.011 0.001 HIS J 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (33108) covalent geometry : angle 0.63305 / 0.34 (45425) hydrogen bonds : bond 0.03696 / 2.40 ( 1033) hydrogen bonds : angle 4.54121 / 3.14 ( 2791) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5177.39 seconds wall clock time: 90 minutes 37.91 seconds (5437.91 seconds total)