Starting phenix.real_space_refine on Thu May 29 07:49:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jay_36138/05_2025/8jay_36138.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jay_36138/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jay_36138/05_2025/8jay_36138.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jay_36138/05_2025/8jay_36138.map" model { file = "/net/cci-nas-00/data/ceres_data/8jay_36138/05_2025/8jay_36138.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jay_36138/05_2025/8jay_36138.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 19.29, per 1000 atoms: 0.60 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: 8.56 Conformation dependent library (CDL) restraints added in 3.6 seconds 6914 Ramachandran restraints generated. 3457 Oldfield, 0 Emsley, 3457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6610 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 43 sheets defined 33.6% alpha, 11.2% beta 48 base pairs and 97 stacking pairs defined. Time for finding SS restraints: 11.28 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: 11.78 Time building geometry restraints manager: 9.61 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: 5.860 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: 0.040 Extract box with map and model: 1.110 Check model and map are aligned: 0.190 Set scattering table: 0.280 Process input model: 76.130 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.150 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.030 ------------------------------------------------------------------------------- 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 : 13.83 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.075 0.002 TRP C 231 HIS 0.006 0.001 HIS N 188 PHE 0.035 0.001 PHE C 245 TYR 0.019 0.001 TYR B 213 ARG 0.015 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.14142 ( 1033) hydrogen bonds : angle 5.73249 ( 2791) covalent geometry : bond 0.00268 (33108) covalent geometry : angle 0.65147 (45425) *********************** 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 : 3.218 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: 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: 0.7638 (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: 0.5866 (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: 0.8040 (ppp) REVERT: D 336 MET cc_start: 0.7330 (mmp) cc_final: 0.6643 (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: 0.5144 (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: M 370 TRP cc_start: 0.6854 (t-100) cc_final: 0.6450 (t-100) REVERT: N 260 GLU cc_start: 0.6309 (pm20) cc_final: 0.5936 (mt-10) REVERT: N 271 LYS cc_start: 0.8197 (mmtt) cc_final: 0.7822 (mmtt) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.4163 time to fit residues: 254.2227 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 : 3.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 6.9990 chunk 272 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 184 optimal weight: 6.9990 chunk 145 optimal weight: 9.9990 chunk 282 optimal weight: 5.9990 chunk 109 optimal weight: 0.3980 chunk 171 optimal weight: 10.0000 chunk 210 optimal weight: 1.9990 chunk 326 optimal weight: 9.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- 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** ** 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 B 109 ASN B 188 HIS I 61 GLN I 90 ASN ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS M 69 ASN M 90 ASN M 329 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.102478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.083875 restraints weight = 123294.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.085520 restraints weight = 79631.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.086667 restraints weight = 59424.193| |-----------------------------------------------------------------------------| r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3445 r_free = 0.3445 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3445 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 33108 Z= 0.186 Angle : 0.665 9.961 45425 Z= 0.343 Chirality : 0.046 0.277 4909 Planarity : 0.004 0.055 5180 Dihedral : 17.164 169.819 5785 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.13 % Allowed : 7.08 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.14), residues: 3457 helix: 0.43 (0.16), residues: 1029 sheet: -1.39 (0.21), residues: 605 loop : -2.31 (0.14), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 46 HIS 0.006 0.001 HIS A 207 PHE 0.021 0.002 PHE C 425 TYR 0.035 0.002 TYR B 213 ARG 0.029 0.001 ARG A 225 Details of bonding type rmsd hydrogen bonds : bond 0.04646 ( 1033) hydrogen bonds : angle 4.89946 ( 2791) covalent geometry : bond 0.00416 (33108) covalent geometry : angle 0.66534 (45425) *********************** 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 338 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 334 time to evaluate : 3.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 ILE cc_start: 0.8645 (mm) cc_final: 0.8182 (tp) REVERT: C 303 MET cc_start: 0.8198 (ptt) cc_final: 0.7984 (ptm) REVERT: A 341 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7386 (tp40) REVERT: A 430 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8138 (tm-30) REVERT: D 133 ASP cc_start: 0.9013 (p0) cc_final: 0.8773 (p0) REVERT: D 277 MET cc_start: 0.8201 (tmm) cc_final: 0.7953 (tmm) REVERT: D 323 ILE cc_start: 0.6576 (pt) cc_final: 0.6112 (pt) REVERT: D 336 MET cc_start: 0.6784 (mmp) cc_final: 0.6550 (mmp) REVERT: B 154 TYR cc_start: 0.7096 (m-10) cc_final: 0.6706 (m-10) REVERT: B 192 TRP cc_start: 0.7308 (p-90) cc_final: 0.6822 (p90) REVERT: I 1 MET cc_start: 0.8277 (mpp) cc_final: 0.7994 (mmm) REVERT: J 262 GLN cc_start: 0.8768 (mp10) cc_final: 0.8389 (mp10) REVERT: J 294 TRP cc_start: 0.6066 (p-90) cc_final: 0.5209 (p-90) REVERT: J 336 MET cc_start: 0.7524 (pmm) cc_final: 0.7202 (pmm) REVERT: M 370 TRP cc_start: 0.6673 (t-100) cc_final: 0.6152 (t-100) REVERT: N 271 LYS cc_start: 0.8116 (mmtt) cc_final: 0.7761 (mmtt) outliers start: 4 outliers final: 0 residues processed: 338 average time/residue: 0.3903 time to fit residues: 215.1904 Evaluate side-chains 250 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 248 time to evaluate : 3.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 193 optimal weight: 0.9990 chunk 158 optimal weight: 0.6980 chunk 140 optimal weight: 0.3980 chunk 233 optimal weight: 0.8980 chunk 221 optimal weight: 0.0980 chunk 289 optimal weight: 4.9990 chunk 218 optimal weight: 5.9990 chunk 262 optimal weight: 0.7980 chunk 220 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 358 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 358 HIS M 69 ASN M 251 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.105958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.086978 restraints weight = 122451.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.088728 restraints weight = 78509.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.089902 restraints weight = 58360.257| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 33108 Z= 0.122 Angle : 0.614 10.487 45425 Z= 0.314 Chirality : 0.044 0.231 4909 Planarity : 0.004 0.072 5180 Dihedral : 17.051 170.543 5785 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.38 % Favored : 92.62 % Rotamer: Outliers : 0.03 % Allowed : 4.41 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.14), residues: 3457 helix: 0.60 (0.16), residues: 1019 sheet: -1.25 (0.21), residues: 614 loop : -2.24 (0.14), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP N 46 HIS 0.006 0.001 HIS J 358 PHE 0.028 0.001 PHE A 403 TYR 0.025 0.001 TYR M 346 ARG 0.009 0.000 ARG D 362 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 1033) hydrogen bonds : angle 4.64043 ( 2791) covalent geometry : bond 0.00263 (33108) covalent geometry : angle 0.61394 (45425) *********************** 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 374 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 373 time to evaluate : 3.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 324 GLU cc_start: 0.6752 (tp30) cc_final: 0.6538 (tp30) REVERT: C 344 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8523 (pm20) REVERT: A 111 HIS cc_start: 0.8130 (p-80) cc_final: 0.7650 (m-70) REVERT: D 92 MET cc_start: 0.7696 (ttp) cc_final: 0.7465 (ttp) REVERT: D 133 ASP cc_start: 0.9010 (p0) cc_final: 0.8776 (p0) REVERT: D 193 ARG cc_start: 0.6162 (tpt170) cc_final: 0.5882 (tpt170) REVERT: D 277 MET cc_start: 0.8198 (tmm) cc_final: 0.7903 (ppp) REVERT: D 323 ILE cc_start: 0.6452 (pt) cc_final: 0.5966 (pt) REVERT: B 192 TRP cc_start: 0.7212 (p-90) cc_final: 0.6618 (p90) REVERT: B 393 LEU cc_start: 0.8777 (mm) cc_final: 0.8562 (mm) REVERT: I 304 PHE cc_start: 0.8529 (t80) cc_final: 0.8324 (t80) REVERT: I 309 ASP cc_start: 0.7744 (t0) cc_final: 0.7526 (t0) REVERT: J 262 GLN cc_start: 0.8598 (mp10) cc_final: 0.8344 (mp10) REVERT: J 294 TRP cc_start: 0.6010 (p-90) cc_final: 0.5002 (p-90) REVERT: J 336 MET cc_start: 0.7444 (pmm) cc_final: 0.7091 (pmm) REVERT: N 271 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7762 (mmtt) outliers start: 1 outliers final: 0 residues processed: 374 average time/residue: 0.4397 time to fit residues: 267.8178 Evaluate side-chains 270 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 269 time to evaluate : 3.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 329 optimal weight: 0.7980 chunk 147 optimal weight: 5.9990 chunk 282 optimal weight: 3.9990 chunk 142 optimal weight: 7.9990 chunk 324 optimal weight: 0.0070 chunk 167 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 305 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- 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** C 360 HIS D 370 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS M 69 ASN ** M 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.104881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.085995 restraints weight = 122057.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.087754 restraints weight = 77597.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.088939 restraints weight = 57199.794| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33108 Z= 0.128 Angle : 0.609 10.618 45425 Z= 0.312 Chirality : 0.045 0.243 4909 Planarity : 0.004 0.058 5180 Dihedral : 17.027 171.134 5785 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.22 % Favored : 91.76 % Rotamer: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.14), residues: 3457 helix: 0.63 (0.17), residues: 1017 sheet: -1.29 (0.21), residues: 607 loop : -2.22 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 192 HIS 0.007 0.001 HIS D 320 PHE 0.019 0.001 PHE I 403 TYR 0.017 0.001 TYR M 346 ARG 0.008 0.000 ARG D 193 Details of bonding type rmsd hydrogen bonds : bond 0.03771 ( 1033) hydrogen bonds : angle 4.53958 ( 2791) covalent geometry : bond 0.00287 (33108) covalent geometry : angle 0.60926 (45425) *********************** 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 : 3.481 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 95 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7272 (tp30) REVERT: C 303 MET cc_start: 0.7937 (ptm) cc_final: 0.7573 (ptm) REVERT: C 476 GLU cc_start: 0.8666 (pm20) cc_final: 0.8209 (pm20) REVERT: A 111 HIS cc_start: 0.8122 (p-80) cc_final: 0.7613 (m-70) REVERT: A 327 GLU cc_start: 0.7583 (tp30) cc_final: 0.7325 (tm-30) REVERT: D 13 GLU cc_start: 0.8510 (pp20) cc_final: 0.8300 (pp20) REVERT: D 14 ASP cc_start: 0.8179 (p0) cc_final: 0.7921 (p0) REVERT: D 74 VAL cc_start: 0.8731 (m) cc_final: 0.8371 (p) REVERT: D 133 ASP cc_start: 0.8954 (p0) cc_final: 0.8732 (p0) REVERT: D 277 MET cc_start: 0.8182 (tmm) cc_final: 0.7883 (tmm) REVERT: D 358 HIS cc_start: 0.5442 (t70) cc_final: 0.5226 (t70) REVERT: B 151 ASN cc_start: 0.7825 (p0) cc_final: 0.7624 (p0) REVERT: B 393 LEU cc_start: 0.8772 (mm) cc_final: 0.8540 (mm) REVERT: J 251 TYR cc_start: 0.6216 (t80) cc_final: 0.5840 (t80) REVERT: J 294 TRP cc_start: 0.6185 (p-90) cc_final: 0.5219 (p-90) REVERT: J 336 MET cc_start: 0.7449 (pmm) cc_final: 0.7094 (pmm) REVERT: J 352 LYS cc_start: 0.7218 (mmtt) cc_final: 0.6953 (mptt) REVERT: J 411 PHE cc_start: 0.7817 (p90) cc_final: 0.7615 (p90) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.3935 time to fit residues: 231.5041 Evaluate side-chains 260 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 3.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 156 optimal weight: 2.9990 chunk 183 optimal weight: 9.9990 chunk 101 optimal weight: 3.9990 chunk 255 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 237 optimal weight: 7.9990 chunk 128 optimal weight: 0.0170 chunk 55 optimal weight: 0.9980 chunk 158 optimal weight: 8.9990 chunk 305 optimal weight: 7.9990 chunk 263 optimal weight: 0.9980 overall best weight: 1.2022 ------------------------------------------------------------------------------- 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** 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 358 HIS M 69 ASN ** M 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.105244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.086853 restraints weight = 120569.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.088496 restraints weight = 78669.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.089588 restraints weight = 59011.613| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3505 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3505 r_free = 0.3505 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3505 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.1573 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= 0.124 Angle : 0.612 11.025 45425 Z= 0.313 Chirality : 0.044 0.212 4909 Planarity : 0.004 0.070 5180 Dihedral : 16.993 171.128 5785 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.90 % Favored : 92.07 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.14), residues: 3457 helix: 0.65 (0.16), residues: 1010 sheet: -1.19 (0.22), residues: 581 loop : -2.20 (0.14), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 33 HIS 0.008 0.001 HIS J 358 PHE 0.020 0.001 PHE C 75 TYR 0.028 0.001 TYR B 213 ARG 0.006 0.000 ARG M 362 Details of bonding type rmsd hydrogen bonds : bond 0.03699 ( 1033) hydrogen bonds : angle 4.50349 ( 2791) covalent geometry : bond 0.00276 (33108) covalent geometry : angle 0.61215 (45425) *********************** 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 358 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 358 time to evaluate : 3.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 ILE cc_start: 0.8220 (mm) cc_final: 0.7952 (tp) REVERT: C 303 MET cc_start: 0.7915 (ptm) cc_final: 0.7624 (ptm) REVERT: A 111 HIS cc_start: 0.8117 (p-80) cc_final: 0.7643 (m-70) REVERT: A 327 GLU cc_start: 0.7528 (tp30) cc_final: 0.7228 (tm-30) REVERT: D 99 ILE cc_start: 0.8735 (pt) cc_final: 0.8189 (mt) REVERT: D 130 ASP cc_start: 0.8680 (p0) cc_final: 0.8443 (p0) REVERT: D 133 ASP cc_start: 0.9009 (p0) cc_final: 0.8755 (p0) REVERT: D 193 ARG cc_start: 0.5419 (tpt170) cc_final: 0.4992 (tpt170) REVERT: D 277 MET cc_start: 0.7969 (tmm) cc_final: 0.7441 (ppp) REVERT: D 323 ILE cc_start: 0.6462 (pt) cc_final: 0.6030 (pt) REVERT: D 401 ILE cc_start: 0.8696 (mt) cc_final: 0.8433 (mm) REVERT: B 151 ASN cc_start: 0.7772 (p0) cc_final: 0.7564 (p0) REVERT: J 251 TYR cc_start: 0.6257 (t80) cc_final: 0.5942 (t80) REVERT: J 294 TRP cc_start: 0.6194 (p-90) cc_final: 0.5221 (p-90) REVERT: J 336 MET cc_start: 0.7597 (pmm) cc_final: 0.7265 (pmm) REVERT: J 352 LYS cc_start: 0.7171 (mmtt) cc_final: 0.6894 (mptt) outliers start: 0 outliers final: 0 residues processed: 358 average time/residue: 0.3995 time to fit residues: 237.1508 Evaluate side-chains 253 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 3.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 52 optimal weight: 5.9990 chunk 101 optimal weight: 0.9980 chunk 315 optimal weight: 5.9990 chunk 210 optimal weight: 0.9980 chunk 301 optimal weight: 5.9990 chunk 328 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 chunk 146 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 199 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- 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 430 GLN D 370 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS M 69 ASN ** M 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 251 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.104791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.086201 restraints weight = 121107.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.087868 restraints weight = 78976.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.088979 restraints weight = 59205.110| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 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 = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.1688 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= 0.136 Angle : 0.621 11.234 45425 Z= 0.317 Chirality : 0.045 0.231 4909 Planarity : 0.004 0.052 5180 Dihedral : 16.991 171.284 5785 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.59 % Favored : 91.38 % Rotamer: Outliers : 0.03 % Allowed : 3.06 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.14), residues: 3457 helix: 0.66 (0.16), residues: 1016 sheet: -1.26 (0.21), residues: 586 loop : -2.22 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 33 HIS 0.009 0.001 HIS J 358 PHE 0.017 0.001 PHE C 503 TYR 0.026 0.001 TYR B 213 ARG 0.005 0.000 ARG M 362 Details of bonding type rmsd hydrogen bonds : bond 0.03725 ( 1033) hydrogen bonds : angle 4.49745 ( 2791) covalent geometry : bond 0.00305 (33108) covalent geometry : angle 0.62126 (45425) *********************** 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 357 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 356 time to evaluate : 3.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 ILE cc_start: 0.8279 (mm) cc_final: 0.7959 (tp) REVERT: C 303 MET cc_start: 0.7897 (ptm) cc_final: 0.7669 (ptm) REVERT: A 225 ARG cc_start: 0.6272 (mpt-90) cc_final: 0.5991 (mtt90) REVERT: A 327 GLU cc_start: 0.7532 (tp30) cc_final: 0.7241 (tm-30) REVERT: A 353 TYR cc_start: 0.7094 (m-80) cc_final: 0.6881 (m-80) REVERT: D 99 ILE cc_start: 0.8675 (pt) cc_final: 0.8155 (mt) REVERT: D 100 ASP cc_start: 0.7919 (t0) cc_final: 0.7367 (t0) REVERT: D 130 ASP cc_start: 0.8708 (p0) cc_final: 0.8454 (p0) REVERT: D 133 ASP cc_start: 0.8949 (p0) cc_final: 0.8725 (p0) REVERT: D 323 ILE cc_start: 0.6469 (pt) cc_final: 0.6012 (pt) REVERT: D 401 ILE cc_start: 0.8708 (mt) cc_final: 0.8490 (mm) REVERT: B 151 ASN cc_start: 0.7689 (p0) cc_final: 0.7458 (p0) REVERT: J 251 TYR cc_start: 0.6206 (t80) cc_final: 0.5987 (t80) REVERT: J 294 TRP cc_start: 0.6161 (p-90) cc_final: 0.5199 (p-90) REVERT: J 336 MET cc_start: 0.7530 (pmm) cc_final: 0.7183 (pmm) REVERT: J 352 LYS cc_start: 0.7055 (mmtt) cc_final: 0.6784 (mptt) REVERT: M 1 MET cc_start: 0.5812 (pmm) cc_final: 0.5519 (pmm) outliers start: 1 outliers final: 0 residues processed: 357 average time/residue: 0.3875 time to fit residues: 228.2386 Evaluate side-chains 249 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 3.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 180 optimal weight: 0.2980 chunk 314 optimal weight: 5.9990 chunk 303 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 127 optimal weight: 10.0000 chunk 313 optimal weight: 6.9990 chunk 149 optimal weight: 10.0000 chunk 212 optimal weight: 0.0020 chunk 29 optimal weight: 5.9990 chunk 230 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 overall best weight: 2.1592 ------------------------------------------------------------------------------- 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** C 360 HIS ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN D 358 HIS D 370 ASN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS ** J 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 69 ASN M 251 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.103862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.085155 restraints weight = 121801.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.086895 restraints weight = 77244.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.088047 restraints weight = 56931.954| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 33108 Z= 0.161 Angle : 0.647 11.694 45425 Z= 0.330 Chirality : 0.046 0.245 4909 Planarity : 0.004 0.051 5180 Dihedral : 17.035 171.246 5785 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.31 % Favored : 90.66 % Rotamer: Outliers : 0.03 % Allowed : 1.77 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.14), residues: 3457 helix: 0.60 (0.16), residues: 1016 sheet: -1.27 (0.21), residues: 582 loop : -2.27 (0.14), residues: 1859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 294 HIS 0.009 0.001 HIS J 358 PHE 0.027 0.002 PHE I 403 TYR 0.024 0.001 TYR B 213 ARG 0.018 0.001 ARG D 283 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 1033) hydrogen bonds : angle 4.56691 ( 2791) covalent geometry : bond 0.00366 (33108) covalent geometry : angle 0.64717 (45425) *********************** 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 360 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 359 time to evaluate : 3.178 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 ILE cc_start: 0.8419 (mm) cc_final: 0.8166 (mm) REVERT: C 95 GLU cc_start: 0.7454 (mm-30) cc_final: 0.7164 (tp30) REVERT: C 303 MET cc_start: 0.7937 (ptm) cc_final: 0.7687 (ptm) REVERT: A 111 HIS cc_start: 0.8057 (p-80) cc_final: 0.7495 (m-70) REVERT: A 327 GLU cc_start: 0.7680 (tp30) cc_final: 0.7332 (tm-30) REVERT: D 74 VAL cc_start: 0.8695 (m) cc_final: 0.8369 (p) REVERT: D 99 ILE cc_start: 0.8773 (pt) cc_final: 0.8570 (mt) REVERT: D 100 ASP cc_start: 0.7999 (t0) cc_final: 0.7496 (t0) REVERT: D 130 ASP cc_start: 0.8721 (p0) cc_final: 0.8469 (p0) REVERT: D 193 ARG cc_start: 0.6173 (tpt170) cc_final: 0.5192 (tpt170) REVERT: D 215 CYS cc_start: 0.6377 (m) cc_final: 0.6156 (m) REVERT: D 277 MET cc_start: 0.8284 (ppp) cc_final: 0.7994 (ppp) REVERT: D 323 ILE cc_start: 0.6552 (pt) cc_final: 0.6133 (pt) REVERT: D 401 ILE cc_start: 0.8712 (mt) cc_final: 0.8472 (mm) REVERT: B 137 LYS cc_start: 0.7945 (ptmm) cc_final: 0.7675 (pptt) REVERT: B 151 ASN cc_start: 0.7683 (p0) cc_final: 0.7455 (p0) REVERT: B 393 LEU cc_start: 0.8814 (mm) cc_final: 0.8587 (mm) REVERT: J 77 GLU cc_start: 0.7513 (tp30) cc_final: 0.7216 (tp30) REVERT: J 251 TYR cc_start: 0.6145 (t80) cc_final: 0.5897 (t80) REVERT: J 262 GLN cc_start: 0.8611 (mp10) cc_final: 0.8266 (mp10) REVERT: J 294 TRP cc_start: 0.6405 (p-90) cc_final: 0.5249 (p-90) REVERT: J 336 MET cc_start: 0.7582 (pmm) cc_final: 0.7188 (pmm) REVERT: J 352 LYS cc_start: 0.7106 (mmtt) cc_final: 0.6837 (mptt) outliers start: 1 outliers final: 0 residues processed: 359 average time/residue: 0.3901 time to fit residues: 230.6110 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 : 3.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 199 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 179 optimal weight: 7.9990 chunk 27 optimal weight: 0.0770 chunk 102 optimal weight: 0.0980 chunk 343 optimal weight: 2.9990 chunk 308 optimal weight: 4.9990 chunk 305 optimal weight: 0.9980 chunk 358 optimal weight: 8.9990 chunk 289 optimal weight: 6.9990 chunk 263 optimal weight: 0.9980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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** D 358 HIS D 370 ASN B 234 ASN ** 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 = 0.3836 r_free = 0.3836 target = 0.106282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.087432 restraints weight = 121849.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.089623 restraints weight = 80455.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.090426 restraints weight = 56596.489| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 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 = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33108 Z= 0.116 Angle : 0.622 11.943 45425 Z= 0.315 Chirality : 0.045 0.229 4909 Planarity : 0.004 0.045 5180 Dihedral : 16.937 171.050 5785 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.49 % Favored : 92.48 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.14), residues: 3457 helix: 0.69 (0.16), residues: 1014 sheet: -1.22 (0.21), residues: 601 loop : -2.20 (0.14), residues: 1842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP B 192 HIS 0.009 0.001 HIS J 358 PHE 0.025 0.001 PHE I 403 TYR 0.027 0.001 TYR B 213 ARG 0.011 0.000 ARG B 189 Details of bonding type rmsd hydrogen bonds : bond 0.03521 ( 1033) hydrogen bonds : angle 4.42209 ( 2791) covalent geometry : bond 0.00251 (33108) covalent geometry : angle 0.62217 (45425) *********************** 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 374 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 374 time to evaluate : 3.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 303 MET cc_start: 0.7765 (ptm) cc_final: 0.7471 (ptm) REVERT: A 111 HIS cc_start: 0.8068 (p-80) cc_final: 0.7672 (m-70) REVERT: A 327 GLU cc_start: 0.7556 (tp30) cc_final: 0.7212 (tm-30) REVERT: A 489 ILE cc_start: 0.9129 (pt) cc_final: 0.8827 (pt) REVERT: D 74 VAL cc_start: 0.8603 (m) cc_final: 0.8275 (p) REVERT: D 100 ASP cc_start: 0.7990 (t0) cc_final: 0.7610 (t70) REVERT: D 277 MET cc_start: 0.8327 (ppp) cc_final: 0.7975 (ppp) REVERT: D 323 ILE cc_start: 0.6451 (pt) cc_final: 0.5977 (pt) REVERT: D 401 ILE cc_start: 0.8680 (mt) cc_final: 0.8408 (mm) REVERT: B 151 ASN cc_start: 0.7510 (p0) cc_final: 0.7302 (p0) REVERT: I 303 MET cc_start: 0.7459 (tpp) cc_final: 0.7090 (tpt) REVERT: J 77 GLU cc_start: 0.7454 (tp30) cc_final: 0.7133 (tp30) REVERT: J 294 TRP cc_start: 0.6295 (p-90) cc_final: 0.5258 (p-90) REVERT: J 336 MET cc_start: 0.7497 (pmm) cc_final: 0.7070 (pmm) REVERT: J 352 LYS cc_start: 0.7061 (mmtt) cc_final: 0.6838 (mptt) outliers start: 0 outliers final: 0 residues processed: 374 average time/residue: 0.4297 time to fit residues: 265.7444 Evaluate side-chains 269 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 3.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 18 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 126 optimal weight: 0.0060 chunk 146 optimal weight: 0.8980 chunk 114 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 278 optimal weight: 6.9990 chunk 35 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 245 optimal weight: 0.5980 chunk 200 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- 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 302 GLN D 358 HIS D 370 ASN ** 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 = 0.3836 r_free = 0.3836 target = 0.106351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.087363 restraints weight = 121108.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.089175 restraints weight = 76419.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.090400 restraints weight = 56253.429| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3511 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3511 r_free = 0.3511 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3511 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33108 Z= 0.117 Angle : 0.627 12.208 45425 Z= 0.317 Chirality : 0.045 0.228 4909 Planarity : 0.004 0.052 5180 Dihedral : 16.903 171.241 5785 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.78 % Favored : 92.19 % Rotamer: Outliers : 0.06 % Allowed : 0.84 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.14), residues: 3457 helix: 0.65 (0.16), residues: 1020 sheet: -1.10 (0.22), residues: 596 loop : -2.21 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 192 HIS 0.010 0.001 HIS J 358 PHE 0.023 0.001 PHE I 403 TYR 0.024 0.001 TYR B 213 ARG 0.013 0.000 ARG B 257 Details of bonding type rmsd hydrogen bonds : bond 0.03418 ( 1033) hydrogen bonds : angle 4.40630 ( 2791) covalent geometry : bond 0.00257 (33108) covalent geometry : angle 0.62693 (45425) *********************** 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 369 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 367 time to evaluate : 3.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 7 ILE cc_start: 0.8024 (mm) cc_final: 0.7777 (mm) REVERT: C 95 GLU cc_start: 0.7260 (tp30) cc_final: 0.7003 (mm-30) REVERT: C 303 MET cc_start: 0.7728 (ptm) cc_final: 0.7435 (ptm) REVERT: C 406 MET cc_start: 0.8164 (tmm) cc_final: 0.7920 (tmm) REVERT: A 74 MET cc_start: 0.5199 (tpt) cc_final: 0.4722 (tpt) REVERT: A 111 HIS cc_start: 0.8093 (p-80) cc_final: 0.7642 (m-70) REVERT: A 302 GLN cc_start: 0.7669 (OUTLIER) cc_final: 0.7003 (pm20) REVERT: A 327 GLU cc_start: 0.7540 (tp30) cc_final: 0.7263 (tm-30) REVERT: D 74 VAL cc_start: 0.8624 (m) cc_final: 0.8291 (p) REVERT: D 277 MET cc_start: 0.8324 (ppp) cc_final: 0.7983 (ppp) REVERT: D 323 ILE cc_start: 0.6469 (pt) cc_final: 0.5988 (pt) REVERT: D 401 ILE cc_start: 0.8651 (mt) cc_final: 0.8356 (mm) REVERT: J 77 GLU cc_start: 0.7429 (tp30) cc_final: 0.7157 (tp30) REVERT: J 262 GLN cc_start: 0.8602 (mp10) cc_final: 0.8287 (mp10) REVERT: J 294 TRP cc_start: 0.6280 (p-90) cc_final: 0.5243 (p-90) REVERT: J 336 MET cc_start: 0.7583 (pmm) cc_final: 0.7203 (pmm) REVERT: J 352 LYS cc_start: 0.7092 (mmtt) cc_final: 0.6854 (mptt) REVERT: M 1 MET cc_start: 0.5633 (pmm) cc_final: 0.5365 (pmm) REVERT: N 403 ILE cc_start: 0.7937 (mm) cc_final: 0.7726 (mp) outliers start: 2 outliers final: 0 residues processed: 368 average time/residue: 0.4057 time to fit residues: 246.3505 Evaluate side-chains 272 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 271 time to evaluate : 3.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 78 optimal weight: 0.9990 chunk 166 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 67 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 340 optimal weight: 9.9990 chunk 241 optimal weight: 0.0970 chunk 57 optimal weight: 4.9990 chunk 276 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 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 370 ASN ** J 357 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 358 HIS J 370 ASN M 69 ASN ** M 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 116 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.103970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.085250 restraints weight = 121986.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.086995 restraints weight = 77973.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.088154 restraints weight = 57611.774| |-----------------------------------------------------------------------------| 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 = 0.72 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 = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2040 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= 0.154 Angle : 0.657 12.459 45425 Z= 0.334 Chirality : 0.046 0.222 4909 Planarity : 0.004 0.051 5180 Dihedral : 16.984 171.447 5785 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.82 % Favored : 91.15 % Rotamer: Outliers : 0.03 % Allowed : 0.48 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.14), residues: 3457 helix: 0.57 (0.16), residues: 1018 sheet: -1.28 (0.21), residues: 600 loop : -2.23 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 192 HIS 0.010 0.001 HIS J 358 PHE 0.028 0.002 PHE I 403 TYR 0.021 0.001 TYR B 213 ARG 0.016 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 1033) hydrogen bonds : angle 4.53483 ( 2791) covalent geometry : bond 0.00347 (33108) covalent geometry : angle 0.65691 (45425) ********************** 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 347 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 3.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 GLU cc_start: 0.7278 (tp30) cc_final: 0.6963 (mm-30) REVERT: C 303 MET cc_start: 0.7803 (ptm) cc_final: 0.7559 (ptm) REVERT: C 476 GLU cc_start: 0.8656 (pm20) cc_final: 0.8137 (pm20) REVERT: A 111 HIS cc_start: 0.8141 (p-80) cc_final: 0.7609 (m-70) REVERT: D 74 VAL cc_start: 0.8677 (m) cc_final: 0.8358 (p) REVERT: D 277 MET cc_start: 0.8379 (ppp) cc_final: 0.8011 (ppp) REVERT: D 323 ILE cc_start: 0.6538 (pt) cc_final: 0.6065 (pt) REVERT: D 401 ILE cc_start: 0.8684 (mt) cc_final: 0.8358 (mm) REVERT: I 280 TYR cc_start: 0.7922 (m-80) cc_final: 0.7663 (m-10) REVERT: J 77 GLU cc_start: 0.7452 (tp30) cc_final: 0.7178 (tp30) REVERT: J 262 GLN cc_start: 0.8603 (mp10) cc_final: 0.8263 (mp10) REVERT: J 294 TRP cc_start: 0.6587 (p-90) cc_final: 0.5400 (p-90) REVERT: J 336 MET cc_start: 0.7616 (pmm) cc_final: 0.7229 (pmm) REVERT: J 382 ARG cc_start: 0.5180 (mmt180) cc_final: 0.4569 (mmt-90) REVERT: M 1 MET cc_start: 0.5703 (pmm) cc_final: 0.5416 (pmm) outliers start: 1 outliers final: 0 residues processed: 346 average time/residue: 0.4060 time to fit residues: 229.9390 Evaluate side-chains 256 residues out of total 3109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 256 time to evaluate : 3.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 11 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 chunk 286 optimal weight: 8.9990 chunk 136 optimal weight: 0.0060 chunk 78 optimal weight: 0.0030 chunk 246 optimal weight: 3.9990 chunk 288 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 200 optimal weight: 0.8980 overall best weight: 1.1808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 66 ASN C 295 GLN ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 ASN ** 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 = 0.3808 r_free = 0.3808 target = 0.104879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.086223 restraints weight = 121625.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.088562 restraints weight = 78647.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.089472 restraints weight = 52343.193| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.71 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3498 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33108 Z= 0.126 Angle : 0.642 12.380 45425 Z= 0.326 Chirality : 0.045 0.220 4909 Planarity : 0.004 0.059 5180 Dihedral : 16.946 171.194 5785 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.13 % Favored : 91.84 % Rotamer: Outliers : 0.03 % Allowed : 0.45 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.14), residues: 3457 helix: 0.61 (0.16), residues: 1014 sheet: -1.26 (0.21), residues: 602 loop : -2.20 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP B 192 HIS 0.010 0.001 HIS J 358 PHE 0.024 0.001 PHE I 403 TYR 0.025 0.001 TYR B 213 ARG 0.013 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03602 ( 1033) hydrogen bonds : angle 4.48249 ( 2791) covalent geometry : bond 0.00282 (33108) covalent geometry : angle 0.64212 (45425) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9912.77 seconds wall clock time: 175 minutes 10.02 seconds (10510.02 seconds total)