Starting phenix.real_space_refine on Tue Aug 26 00:07:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jay_36138/08_2025/8jay_36138.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jay_36138/08_2025/8jay_36138.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jay_36138/08_2025/8jay_36138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jay_36138/08_2025/8jay_36138.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jay_36138/08_2025/8jay_36138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jay_36138/08_2025/8jay_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-2.0-5787/lib/python3.9/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: 6.55, per 1000 atoms: 0.20 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: 2.32 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6610 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 43 sheets defined 33.6% alpha, 11.2% beta 48 base pairs and 97 stacking pairs defined. Time for finding SS restraints: 3.02 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: 5.29 Time building geometry restraints manager: 3.15 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=" CD GLU C 344 " pdb=" OE1 GLU C 344 " ideal model delta sigma weight residual 1.249 1.219 0.030 1.90e-02 2.77e+03 2.49e+00 bond pdb=" CB GLN C 430 " pdb=" CG GLN C 430 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.06e+00 bond pdb=" CB ARG C 243 " pdb=" CG ARG C 243 " ideal model delta sigma weight residual 1.520 1.479 0.041 3.00e-02 1.11e+03 1.89e+00 bond pdb=" CA GLN C 430 " pdb=" CB GLN C 430 " ideal model delta sigma weight residual 1.530 1.552 -0.022 1.69e-02 3.50e+03 1.69e+00 bond pdb=" C3' DC L 19 " pdb=" O3' DC L 19 " ideal model delta sigma weight residual 1.422 1.461 -0.039 3.00e-02 1.11e+03 1.66e+00 ... (remaining 33103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 44879 2.48 - 4.97: 481 4.97 - 7.45: 55 7.45 - 9.94: 8 9.94 - 12.42: 2 Bond angle restraints: 45425 Sorted by residual: angle pdb=" N GLU C 344 " pdb=" CA GLU C 344 " pdb=" CB GLU C 344 " ideal model delta sigma weight residual 110.28 117.45 -7.17 1.55e+00 4.16e-01 2.14e+01 angle pdb=" N ILE D 348 " pdb=" CA ILE D 348 " pdb=" C ILE D 348 " ideal model delta sigma weight residual 112.96 108.65 4.31 1.00e+00 1.00e+00 1.86e+01 angle pdb=" CA LEU D 39 " pdb=" CB LEU D 39 " pdb=" CG LEU D 39 " ideal model delta sigma weight residual 116.30 128.72 -12.42 3.50e+00 8.16e-02 1.26e+01 angle pdb=" CA GLN C 430 " pdb=" CB GLN C 430 " pdb=" CG GLN C 430 " ideal model delta sigma weight residual 114.10 121.05 -6.95 2.00e+00 2.50e-01 1.21e+01 angle pdb=" C LEU C 343 " pdb=" N GLU C 344 " pdb=" CA GLU C 344 " ideal model delta sigma weight residual 120.31 115.04 5.27 1.52e+00 4.33e-01 1.20e+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 - 0.043: 3579 0.043 - 0.086: 970 0.086 - 0.129: 321 0.129 - 0.172: 29 0.172 - 0.215: 10 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 2.46 2.24 0.21 2.00e-01 2.50e+01 1.15e+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 chirality pdb=" P U O 1 " pdb=" OP1 U O 1 " pdb=" OP2 U O 1 " pdb=" O5' U O 1 " both_signs ideal model delta sigma weight residual True 2.17 2.38 -0.21 2.00e-01 2.50e+01 1.08e+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: 6.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 26.630 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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= 0.129 Angle : 0.651 12.423 45425 Z= 0.337 Chirality : 0.044 0.215 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 aren 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 covalent geometry : bond 0.00268 (33108) covalent geometry : angle 0.65147 (45425) hydrogen bonds : bond 0.14142 ( 1033) hydrogen bonds : angle 5.73249 ( 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 : 1.316 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: 0.2184 time to fit residues: 133.5879 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 : 1.165 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: C 207 HIS ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 GLN A 341 GLN A 430 GLN D 357 GLN D 370 ASN ** 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 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3734 r_free = 0.3734 target = 0.100432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.082014 restraints weight = 126206.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.083631 restraints weight = 81545.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.084712 restraints weight = 60959.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.085438 restraints weight = 50114.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.085845 restraints weight = 43992.653| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 33108 Z= 0.261 Angle : 0.746 10.213 45425 Z= 0.385 Chirality : 0.049 0.345 4909 Planarity : 0.005 0.064 5180 Dihedral : 17.327 170.344 5785 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.46 % Favored : 88.54 % Rotamer: Outliers : 0.26 % Allowed : 8.17 % Favored : 91.57 % 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 aren not related in a simple way. whole: -2.18 (0.14), residues: 3457 helix: 0.22 (0.16), residues: 1028 sheet: -1.75 (0.21), residues: 610 loop : -2.40 (0.14), residues: 1819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 225 TYR 0.041 0.002 TYR A 353 PHE 0.025 0.002 PHE C 503 TRP 0.020 0.002 TRP N 46 HIS 0.008 0.002 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00590 (33108) covalent geometry : angle 0.74568 (45425) hydrogen bonds : bond 0.05275 ( 1033) hydrogen bonds : angle 5.13437 ( 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 327 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 319 time to evaluate : 1.293 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 303 MET cc_start: 0.8280 (ptt) cc_final: 0.8040 (ptm) REVERT: C 364 ARG cc_start: 0.6578 (OUTLIER) cc_final: 0.4071 (mtm-85) REVERT: A 341 GLN cc_start: 0.8516 (OUTLIER) cc_final: 0.7314 (tp40) REVERT: A 430 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.8551 (tm-30) REVERT: D 133 ASP cc_start: 0.8998 (p0) cc_final: 0.8775 (p0) REVERT: D 193 ARG cc_start: 0.6295 (tpt170) cc_final: 0.5733 (tpt170) REVERT: D 277 MET cc_start: 0.8231 (tmm) cc_final: 0.7958 (tmm) REVERT: D 323 ILE cc_start: 0.6662 (pt) cc_final: 0.6242 (pt) REVERT: D 336 MET cc_start: 0.6888 (mmp) cc_final: 0.6652 (mmp) REVERT: B 151 ASN cc_start: 0.7658 (p0) cc_final: 0.7455 (p0) REVERT: B 192 TRP cc_start: 0.7297 (p-90) cc_final: 0.6814 (p90) REVERT: J 262 GLN cc_start: 0.8747 (mp10) cc_final: 0.8353 (mp10) REVERT: J 294 TRP cc_start: 0.6053 (p-90) cc_final: 0.5173 (p-90) REVERT: J 336 MET cc_start: 0.7546 (pmm) cc_final: 0.7255 (pmm) REVERT: N 271 LYS cc_start: 0.8121 (mmtt) cc_final: 0.7787 (mmtt) outliers start: 8 outliers final: 1 residues processed: 326 average time/residue: 0.2092 time to fit residues: 111.3638 Evaluate side-chains 238 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 234 time to evaluate : 0.881 ------------------------------------------------------------------------------- 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: 0.4980 chunk 47 optimal weight: 6.9990 chunk 346 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 324 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 44 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 227 optimal weight: 0.1980 chunk 198 optimal weight: 0.0770 chunk 203 optimal weight: 8.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 188 HIS D 370 ASN B 109 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 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 = 0.105128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.086266 restraints weight = 121791.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.088061 restraints weight = 77436.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.089225 restraints weight = 56962.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.090015 restraints weight = 46537.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.090470 restraints weight = 40527.346| |-----------------------------------------------------------------------------| r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 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 = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 33108 Z= 0.126 Angle : 0.633 10.480 45425 Z= 0.324 Chirality : 0.045 0.264 4909 Planarity : 0.004 0.096 5180 Dihedral : 17.088 170.153 5785 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.06 % Allowed : 4.73 % Favored : 95.21 % 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 aren not related in a simple way. whole: -1.87 (0.14), residues: 3457 helix: 0.41 (0.16), residues: 1033 sheet: -1.29 (0.21), residues: 594 loop : -2.28 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 243 TYR 0.023 0.001 TYR M 346 PHE 0.032 0.002 PHE A 403 TRP 0.013 0.001 TRP B 192 HIS 0.006 0.001 HIS J 358 Details of bonding type rmsd covalent geometry : bond 0.00274 (33108) covalent geometry : angle 0.63323 (45425) hydrogen bonds : bond 0.04029 ( 1033) hydrogen bonds : angle 4.70113 ( 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 375 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 373 time to evaluate : 1.247 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 344 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8619 (pm20) REVERT: C 474 ASP cc_start: 0.7120 (t0) cc_final: 0.6919 (t0) REVERT: A 111 HIS cc_start: 0.8069 (p-80) cc_final: 0.7646 (m-70) REVERT: D 74 VAL cc_start: 0.8650 (m) cc_final: 0.8292 (p) REVERT: D 193 ARG cc_start: 0.6074 (tpt170) cc_final: 0.5760 (tpt170) REVERT: D 277 MET cc_start: 0.8226 (tmm) cc_final: 0.7932 (ppp) REVERT: D 401 ILE cc_start: 0.8717 (mt) cc_final: 0.8477 (mm) REVERT: B 192 TRP cc_start: 0.7138 (p-90) cc_final: 0.6476 (p90) REVERT: I 303 MET cc_start: 0.7400 (tpp) cc_final: 0.7157 (tpt) REVERT: I 304 PHE cc_start: 0.8611 (t80) cc_final: 0.8351 (t80) REVERT: J 262 GLN cc_start: 0.8628 (mp10) cc_final: 0.8341 (mp10) REVERT: J 294 TRP cc_start: 0.6156 (p-90) cc_final: 0.5140 (p-90) REVERT: J 336 MET cc_start: 0.7304 (pmm) cc_final: 0.6966 (pmm) REVERT: N 271 LYS cc_start: 0.8133 (mmtt) cc_final: 0.7751 (mmtt) outliers start: 2 outliers final: 0 residues processed: 375 average time/residue: 0.2030 time to fit residues: 123.6013 Evaluate side-chains 263 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 262 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 206 optimal weight: 9.9990 chunk 258 optimal weight: 10.0000 chunk 246 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 chunk 245 optimal weight: 7.9990 chunk 205 optimal weight: 0.6980 chunk 156 optimal weight: 0.8980 chunk 201 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 222 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 340 HIS ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS M 69 ASN M 251 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.104477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.085530 restraints weight = 122202.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.087235 restraints weight = 78809.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.088409 restraints weight = 58752.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.089170 restraints weight = 48027.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.089670 restraints weight = 42118.376| |-----------------------------------------------------------------------------| 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 = 0.72 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 = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3501 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1539 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= 0.139 Angle : 0.619 10.522 45425 Z= 0.318 Chirality : 0.045 0.241 4909 Planarity : 0.004 0.060 5180 Dihedral : 17.071 170.806 5785 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.74 % Favored : 91.24 % Rotamer: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.85 (0.14), residues: 3457 helix: 0.49 (0.16), residues: 1023 sheet: -1.39 (0.21), residues: 606 loop : -2.26 (0.14), residues: 1828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 481 TYR 0.017 0.001 TYR M 346 PHE 0.018 0.001 PHE C 425 TRP 0.026 0.001 TRP N 46 HIS 0.009 0.001 HIS D 320 Details of bonding type rmsd covalent geometry : bond 0.00312 (33108) covalent geometry : angle 0.61930 (45425) hydrogen bonds : bond 0.03926 ( 1033) hydrogen bonds : angle 4.63387 ( 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 358 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 1.296 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: 0.8061 (ptt) cc_final: 0.7857 (ptm) REVERT: A 111 HIS cc_start: 0.8078 (p-80) cc_final: 0.7606 (m-70) REVERT: A 327 GLU cc_start: 0.7596 (tp30) cc_final: 0.7345 (tm-30) REVERT: D 277 MET cc_start: 0.8199 (tmm) cc_final: 0.7873 (tmm) REVERT: D 323 ILE cc_start: 0.6503 (pt) cc_final: 0.6116 (pt) REVERT: D 401 ILE cc_start: 0.8706 (mt) cc_final: 0.8459 (mm) REVERT: I 309 ASP cc_start: 0.7820 (t0) cc_final: 0.7593 (t0) REVERT: J 262 GLN cc_start: 0.8570 (mp10) cc_final: 0.8368 (mp10) REVERT: J 294 TRP cc_start: 0.6333 (p-90) cc_final: 0.5294 (p-90) REVERT: J 336 MET cc_start: 0.7331 (pmm) cc_final: 0.7019 (pmm) REVERT: J 411 PHE cc_start: 0.7979 (p90) cc_final: 0.7732 (p90) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.1931 time to fit residues: 113.5542 Evaluate side-chains 255 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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: 0.4980 chunk 276 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 350 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 320 optimal weight: 20.0000 chunk 9 optimal weight: 0.8980 chunk 190 optimal weight: 0.5980 chunk 246 optimal weight: 0.3980 chunk 339 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS ** 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 358 HIS M 69 ASN M 251 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.106222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.087161 restraints weight = 122221.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.088924 restraints weight = 78364.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.090110 restraints weight = 58190.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.090895 restraints weight = 47501.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.091419 restraints weight = 41590.109| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3537 r_free = 0.3537 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33108 Z= 0.116 Angle : 0.612 11.122 45425 Z= 0.312 Chirality : 0.044 0.211 4909 Planarity : 0.004 0.075 5180 Dihedral : 16.986 170.749 5785 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.23 % Favored : 92.74 % Rotamer: Outliers : 0.06 % Allowed : 3.15 % Favored : 96.78 % 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 aren not related in a simple way. whole: -1.72 (0.14), residues: 3457 helix: 0.64 (0.17), residues: 1006 sheet: -1.21 (0.21), residues: 594 loop : -2.22 (0.14), residues: 1857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 361 TYR 0.017 0.001 TYR N 190 PHE 0.016 0.001 PHE C 425 TRP 0.015 0.001 TRP N 46 HIS 0.007 0.001 HIS J 358 Details of bonding type rmsd covalent geometry : bond 0.00251 (33108) covalent geometry : angle 0.61193 (45425) hydrogen bonds : bond 0.03610 ( 1033) hydrogen bonds : angle 4.51191 ( 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 386 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 384 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 111 HIS cc_start: 0.8017 (p-80) cc_final: 0.7560 (m-70) REVERT: A 327 GLU cc_start: 0.7481 (tp30) cc_final: 0.7242 (tm-30) REVERT: D 74 VAL cc_start: 0.8520 (m) cc_final: 0.8142 (p) REVERT: D 99 ILE cc_start: 0.8738 (pt) cc_final: 0.8283 (mt) REVERT: D 100 ASP cc_start: 0.7940 (t0) cc_final: 0.7546 (t0) REVERT: D 133 ASP cc_start: 0.8969 (p0) cc_final: 0.8738 (p0) REVERT: D 277 MET cc_start: 0.8092 (tmm) cc_final: 0.7680 (ppp) REVERT: D 323 ILE cc_start: 0.6415 (pt) cc_final: 0.5914 (pt) REVERT: D 401 ILE cc_start: 0.8668 (mt) cc_final: 0.8395 (mm) REVERT: B 151 ASN cc_start: 0.7636 (p0) cc_final: 0.7412 (p0) REVERT: B 153 LEU cc_start: 0.7518 (tp) cc_final: 0.7301 (tp) REVERT: B 273 PHE cc_start: 0.7471 (t80) cc_final: 0.6735 (t80) REVERT: I 309 ASP cc_start: 0.7651 (t0) cc_final: 0.7442 (t0) REVERT: J 251 TYR cc_start: 0.6226 (t80) cc_final: 0.5836 (t80) REVERT: J 294 TRP cc_start: 0.6115 (p-90) cc_final: 0.5219 (p-90) REVERT: J 336 MET cc_start: 0.7486 (pmm) cc_final: 0.7120 (pmm) REVERT: J 411 PHE cc_start: 0.7849 (p90) cc_final: 0.7624 (p90) outliers start: 2 outliers final: 0 residues processed: 386 average time/residue: 0.1790 time to fit residues: 114.4334 Evaluate side-chains 279 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 99 optimal weight: 0.9980 chunk 267 optimal weight: 2.9990 chunk 74 optimal weight: 9.9990 chunk 288 optimal weight: 6.9990 chunk 210 optimal weight: 0.9980 chunk 230 optimal weight: 8.9990 chunk 227 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 6 optimal weight: 2.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 ASN C 129 ASN ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 HIS C 374 ASN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 HIS A 430 GLN D 188 HIS D 370 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS M 69 ASN M 251 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.102264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.083673 restraints weight = 123105.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.085339 restraints weight = 79150.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.086458 restraints weight = 58872.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.087208 restraints weight = 48181.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.087704 restraints weight = 42209.608| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 33108 Z= 0.208 Angle : 0.696 11.335 45425 Z= 0.358 Chirality : 0.047 0.263 4909 Planarity : 0.004 0.057 5180 Dihedral : 17.149 171.474 5785 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.12 % Favored : 89.85 % Rotamer: Outliers : 0.06 % Allowed : 3.31 % Favored : 96.62 % 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 aren not related in a simple way. whole: -1.99 (0.14), residues: 3457 helix: 0.40 (0.16), residues: 1022 sheet: -1.49 (0.21), residues: 593 loop : -2.34 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 283 TYR 0.036 0.002 TYR B 293 PHE 0.029 0.002 PHE I 403 TRP 0.029 0.002 TRP D 33 HIS 0.009 0.001 HIS J 358 Details of bonding type rmsd covalent geometry : bond 0.00473 (33108) covalent geometry : angle 0.69563 (45425) hydrogen bonds : bond 0.04509 ( 1033) hydrogen bonds : angle 4.74515 ( 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 350 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 348 time to evaluate : 1.203 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 1 MET cc_start: 0.2918 (tpt) cc_final: 0.2270 (tpt) REVERT: C 36 ILE cc_start: 0.8490 (mm) cc_final: 0.8087 (tp) REVERT: D 74 VAL cc_start: 0.8725 (m) cc_final: 0.8406 (p) REVERT: D 99 ILE cc_start: 0.8738 (pt) cc_final: 0.8266 (mt) REVERT: D 102 ASN cc_start: 0.8173 (m110) cc_final: 0.7967 (m110) REVERT: D 188 HIS cc_start: 0.7378 (t70) cc_final: 0.7097 (t-170) REVERT: D 323 ILE cc_start: 0.6570 (pt) cc_final: 0.6137 (pt) REVERT: D 401 ILE cc_start: 0.8771 (mt) cc_final: 0.8469 (mm) REVERT: B 151 ASN cc_start: 0.7721 (p0) cc_final: 0.7504 (p0) REVERT: B 153 LEU cc_start: 0.7942 (tp) cc_final: 0.7700 (tp) REVERT: I 280 TYR cc_start: 0.8184 (m-80) cc_final: 0.7908 (m-10) REVERT: J 251 TYR cc_start: 0.6281 (t80) cc_final: 0.5853 (t80) REVERT: J 294 TRP cc_start: 0.6372 (p-90) cc_final: 0.5168 (p-90) REVERT: J 336 MET cc_start: 0.7503 (pmm) cc_final: 0.7116 (pmm) REVERT: M 1 MET cc_start: 0.5891 (pmm) cc_final: 0.5677 (pmm) outliers start: 2 outliers final: 0 residues processed: 349 average time/residue: 0.1916 time to fit residues: 109.5345 Evaluate side-chains 261 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 169 optimal weight: 6.9990 chunk 348 optimal weight: 7.9990 chunk 264 optimal weight: 6.9990 chunk 167 optimal weight: 4.9990 chunk 254 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 209 optimal weight: 6.9990 chunk 237 optimal weight: 9.9990 chunk 224 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 314 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 18 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS D 370 ASN B 109 ASN ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS M 69 ASN ** M 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 295 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.099208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.080923 restraints weight = 125592.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.082528 restraints weight = 81108.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.083606 restraints weight = 60499.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.084322 restraints weight = 49538.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.084794 restraints weight = 43491.561| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3402 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3402 r_free = 0.3402 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3402 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 33108 Z= 0.290 Angle : 0.808 11.306 45425 Z= 0.419 Chirality : 0.051 0.351 4909 Planarity : 0.005 0.097 5180 Dihedral : 17.470 171.258 5785 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.80 % Favored : 88.20 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % 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 aren not related in a simple way. whole: -2.48 (0.14), residues: 3457 helix: -0.02 (0.16), residues: 1020 sheet: -2.01 (0.21), residues: 563 loop : -2.56 (0.13), residues: 1874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG M 362 TYR 0.048 0.003 TYR M 472 PHE 0.032 0.003 PHE I 403 TRP 0.018 0.002 TRP N 124 HIS 0.010 0.002 HIS D 188 Details of bonding type rmsd covalent geometry : bond 0.00658 (33108) covalent geometry : angle 0.80829 (45425) hydrogen bonds : bond 0.05473 ( 1033) hydrogen bonds : angle 5.21640 ( 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 320 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 1.065 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: 0.2923 (tpt) cc_final: 0.2225 (tpt) REVERT: C 95 GLU cc_start: 0.7545 (tp30) cc_final: 0.7195 (tp30) REVERT: A 225 ARG cc_start: 0.6964 (mtt180) cc_final: 0.6239 (mtt180) REVERT: A 353 TYR cc_start: 0.7236 (m-80) cc_final: 0.6901 (m-80) REVERT: D 34 CYS cc_start: 0.8528 (t) cc_final: 0.8304 (t) REVERT: D 99 ILE cc_start: 0.8764 (pt) cc_final: 0.8408 (mt) REVERT: D 401 ILE cc_start: 0.8813 (mt) cc_final: 0.8543 (mm) REVERT: B 151 ASN cc_start: 0.7749 (p0) cc_final: 0.7509 (p0) REVERT: I 303 MET cc_start: 0.8092 (tpp) cc_final: 0.7883 (tpt) REVERT: J 262 GLN cc_start: 0.8766 (mp10) cc_final: 0.8502 (mp10) REVERT: J 287 MET cc_start: 0.6332 (mmm) cc_final: 0.6065 (mmm) REVERT: J 294 TRP cc_start: 0.6532 (p-90) cc_final: 0.5321 (p-90) REVERT: J 336 MET cc_start: 0.7585 (pmm) cc_final: 0.7186 (pmm) REVERT: J 345 MET cc_start: 0.7639 (pmm) cc_final: 0.7413 (pmm) REVERT: M 1 MET cc_start: 0.6161 (pmm) cc_final: 0.5935 (pmm) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.1907 time to fit residues: 101.0128 Evaluate side-chains 240 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 1.131 ------------------------------------------------------------------------------- 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: 7.9990 chunk 42 optimal weight: 0.7980 chunk 236 optimal weight: 7.9990 chunk 217 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 258 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 264 optimal weight: 4.9990 chunk 355 optimal weight: 4.9990 chunk 235 optimal weight: 7.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 ASN ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS D 370 ASN J 163 GLN ** 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 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.100734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.082400 restraints weight = 123381.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.084070 restraints weight = 78967.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.085143 restraints weight = 58487.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.085909 restraints weight = 48047.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.086401 restraints weight = 41947.285| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 33108 Z= 0.202 Angle : 0.719 11.791 45425 Z= 0.371 Chirality : 0.048 0.321 4909 Planarity : 0.004 0.054 5180 Dihedral : 17.371 170.008 5785 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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 aren not related in a simple way. whole: -2.37 (0.14), residues: 3457 helix: 0.13 (0.16), residues: 1022 sheet: -1.96 (0.21), residues: 559 loop : -2.52 (0.14), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 362 TYR 0.031 0.002 TYR A 37 PHE 0.027 0.002 PHE I 403 TRP 0.041 0.002 TRP B 192 HIS 0.007 0.001 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00457 (33108) covalent geometry : angle 0.71929 (45425) hydrogen bonds : bond 0.04749 ( 1033) hydrogen bonds : angle 4.97257 ( 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 331 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 0.952 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: 0.3043 (tpt) cc_final: 0.2286 (tpt) REVERT: C 36 ILE cc_start: 0.8585 (mm) cc_final: 0.8265 (mm) REVERT: C 95 GLU cc_start: 0.7383 (tp30) cc_final: 0.7071 (tp30) REVERT: C 133 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7985 (tt0) REVERT: A 1 MET cc_start: 0.5481 (tpp) cc_final: 0.5098 (tpp) REVERT: A 353 TYR cc_start: 0.6867 (m-80) cc_final: 0.6665 (m-80) REVERT: D 34 CYS cc_start: 0.8490 (t) cc_final: 0.8246 (t) REVERT: D 99 ILE cc_start: 0.8763 (pt) cc_final: 0.8416 (mt) REVERT: D 323 ILE cc_start: 0.6648 (pt) cc_final: 0.6333 (pt) REVERT: D 401 ILE cc_start: 0.8766 (mt) cc_final: 0.8508 (mm) REVERT: B 151 ASN cc_start: 0.7543 (p0) cc_final: 0.7310 (p0) REVERT: I 303 MET cc_start: 0.8131 (tpp) cc_final: 0.7801 (tpt) REVERT: J 262 GLN cc_start: 0.8703 (mp10) cc_final: 0.8485 (mp10) REVERT: J 294 TRP cc_start: 0.6612 (p-90) cc_final: 0.5431 (p-90) REVERT: J 336 MET cc_start: 0.7464 (pmm) cc_final: 0.7127 (pmm) REVERT: J 345 MET cc_start: 0.7694 (pmm) cc_final: 0.7461 (pmm) REVERT: J 382 ARG cc_start: 0.5531 (mmt180) cc_final: 0.5129 (mmt-90) REVERT: M 1 MET cc_start: 0.6123 (pmm) cc_final: 0.5909 (pmm) outliers start: 0 outliers final: 0 residues processed: 331 average time/residue: 0.1769 time to fit residues: 96.9994 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 : 1.203 ------------------------------------------------------------------------------- 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: 4.9990 chunk 282 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 317 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 300 optimal weight: 2.9990 chunk 328 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 146 optimal weight: 0.0980 chunk 232 optimal weight: 0.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN ** C 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 430 GLN D 358 HIS D 370 ASN J 163 GLN ** 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 236 ASN ** 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 = 0.3757 r_free = 0.3757 target = 0.102101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.083608 restraints weight = 122332.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.085319 restraints weight = 77937.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.086442 restraints weight = 57656.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.087198 restraints weight = 47104.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.087714 restraints weight = 41134.183| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 33108 Z= 0.154 Angle : 0.684 12.158 45425 Z= 0.351 Chirality : 0.047 0.268 4909 Planarity : 0.004 0.055 5180 Dihedral : 17.256 169.957 5785 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.66 % Favored : 90.34 % Rotamer: Outliers : 0.03 % Allowed : 0.90 % Favored : 99.07 % 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 aren not related in a simple way. whole: -2.18 (0.14), residues: 3457 helix: 0.24 (0.16), residues: 1022 sheet: -1.72 (0.21), residues: 583 loop : -2.42 (0.14), residues: 1852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 283 TYR 0.027 0.002 TYR B 213 PHE 0.026 0.002 PHE I 403 TRP 0.032 0.002 TRP D 175 HIS 0.008 0.001 HIS J 358 Details of bonding type rmsd covalent geometry : bond 0.00348 (33108) covalent geometry : angle 0.68414 (45425) hydrogen bonds : bond 0.04284 ( 1033) hydrogen bonds : angle 4.83174 ( 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 330 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 329 time to evaluate : 0.848 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: A 1 MET cc_start: 0.5421 (tpp) cc_final: 0.5038 (tpp) REVERT: A 8 GLU cc_start: 0.8203 (pp20) cc_final: 0.7788 (pp20) REVERT: A 111 HIS cc_start: 0.8109 (p-80) cc_final: 0.7453 (m-70) REVERT: D 74 VAL cc_start: 0.8437 (m) cc_final: 0.8143 (p) REVERT: D 323 ILE cc_start: 0.6555 (pt) cc_final: 0.6160 (pt) REVERT: D 401 ILE cc_start: 0.8722 (mt) cc_final: 0.8476 (mm) REVERT: B 151 ASN cc_start: 0.7433 (p0) cc_final: 0.7212 (p0) REVERT: I 303 MET cc_start: 0.8010 (tpp) cc_final: 0.7701 (tpt) REVERT: J 251 TYR cc_start: 0.6037 (t80) cc_final: 0.5618 (t80) REVERT: J 262 GLN cc_start: 0.8658 (mp10) cc_final: 0.8458 (mp10) REVERT: J 287 MET cc_start: 0.6514 (mmm) cc_final: 0.6313 (mmm) REVERT: J 294 TRP cc_start: 0.6593 (p-90) cc_final: 0.5380 (p-90) REVERT: J 336 MET cc_start: 0.7413 (pmm) cc_final: 0.7045 (pmm) REVERT: J 345 MET cc_start: 0.7743 (pmm) cc_final: 0.7507 (pmm) REVERT: J 382 ARG cc_start: 0.5544 (mmt180) cc_final: 0.5132 (mmt-90) REVERT: N 403 ILE cc_start: 0.8038 (mm) cc_final: 0.7793 (mp) outliers start: 1 outliers final: 1 residues processed: 329 average time/residue: 0.1812 time to fit residues: 99.0472 Evaluate side-chains 260 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 259 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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: 0.6980 chunk 19 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 345 optimal weight: 8.9990 chunk 83 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 chunk 273 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 170 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN ** 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 358 HIS D 370 ASN ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.104160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.085359 restraints weight = 122783.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.087114 restraints weight = 77783.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.088272 restraints weight = 57436.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.089049 restraints weight = 46920.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.089569 restraints weight = 41020.244| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.2309 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 : 0.666 12.457 45425 Z= 0.340 Chirality : 0.046 0.267 4909 Planarity : 0.004 0.054 5180 Dihedral : 17.117 170.040 5785 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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 aren not related in a simple way. whole: -2.04 (0.14), residues: 3457 helix: 0.28 (0.16), residues: 1028 sheet: -1.50 (0.21), residues: 599 loop : -2.35 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 189 TYR 0.028 0.001 TYR B 213 PHE 0.020 0.001 PHE N 135 TRP 0.033 0.001 TRP B 192 HIS 0.008 0.001 HIS J 358 Details of bonding type rmsd covalent geometry : bond 0.00280 (33108) covalent geometry : angle 0.66584 (45425) hydrogen bonds : bond 0.03848 ( 1033) hydrogen bonds : angle 4.66750 ( 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 346 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 1.112 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: A 1 MET cc_start: 0.5275 (tpp) cc_final: 0.4979 (tpp) REVERT: A 8 GLU cc_start: 0.8185 (pp20) cc_final: 0.7868 (pp20) REVERT: A 111 HIS cc_start: 0.8046 (p-80) cc_final: 0.7425 (m-70) REVERT: D 34 CYS cc_start: 0.8254 (t) cc_final: 0.8040 (t) REVERT: D 74 VAL cc_start: 0.8370 (m) cc_final: 0.8082 (p) REVERT: D 92 MET cc_start: 0.7652 (ttp) cc_final: 0.7428 (ttp) REVERT: D 323 ILE cc_start: 0.6494 (pt) cc_final: 0.6105 (pt) REVERT: D 401 ILE cc_start: 0.8692 (mt) cc_final: 0.8352 (mm) REVERT: B 151 ASN cc_start: 0.7322 (p0) cc_final: 0.7117 (p0) REVERT: I 243 ARG cc_start: 0.6148 (mtp180) cc_final: 0.5592 (mtp180) REVERT: J 262 GLN cc_start: 0.8596 (mp10) cc_final: 0.8392 (mp10) REVERT: J 294 TRP cc_start: 0.6627 (p-90) cc_final: 0.5401 (p-90) REVERT: J 336 MET cc_start: 0.7460 (pmm) cc_final: 0.7060 (pmm) REVERT: J 345 MET cc_start: 0.7793 (pmm) cc_final: 0.7561 (pmm) REVERT: J 352 LYS cc_start: 0.6826 (mmtt) cc_final: 0.6409 (mmtm) REVERT: J 382 ARG cc_start: 0.5359 (mmt180) cc_final: 0.4902 (mmt-90) REVERT: N 122 LYS cc_start: 0.7386 (mmtm) cc_final: 0.7184 (mmtt) REVERT: N 403 ILE cc_start: 0.8048 (mm) cc_final: 0.7797 (mp) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.1730 time to fit residues: 99.3533 Evaluate side-chains 263 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 137 optimal weight: 0.9990 chunk 253 optimal weight: 6.9990 chunk 245 optimal weight: 0.8980 chunk 344 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 107 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 203 optimal weight: 1.9990 chunk 278 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 129 ASN C 295 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 ASN ** B 320 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.102650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.084180 restraints weight = 122700.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.085869 restraints weight = 78208.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.086984 restraints weight = 57946.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.087745 restraints weight = 47453.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.088188 restraints weight = 41418.080| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3471 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 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 = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33108 Z= 0.158 Angle : 0.679 12.417 45425 Z= 0.347 Chirality : 0.047 0.261 4909 Planarity : 0.004 0.077 5180 Dihedral : 17.157 170.785 5785 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.66 % Favored : 90.31 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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 aren not related in a simple way. whole: -2.05 (0.14), residues: 3457 helix: 0.30 (0.16), residues: 1028 sheet: -1.47 (0.21), residues: 580 loop : -2.38 (0.14), residues: 1849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 186 TYR 0.023 0.002 TYR J 171 PHE 0.030 0.002 PHE A 403 TRP 0.061 0.002 TRP C 86 HIS 0.008 0.001 HIS J 358 Details of bonding type rmsd covalent geometry : bond 0.00360 (33108) covalent geometry : angle 0.67901 (45425) hydrogen bonds : bond 0.04118 ( 1033) hydrogen bonds : angle 4.68488 ( 2791) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5232.67 seconds wall clock time: 91 minutes 34.55 seconds (5494.55 seconds total)