Starting phenix.real_space_refine on Thu Sep 18 13:05:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j36_61107/09_2025/9j36_61107.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j36_61107/09_2025/9j36_61107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j36_61107/09_2025/9j36_61107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j36_61107/09_2025/9j36_61107.map" model { file = "/net/cci-nas-00/data/ceres_data/9j36_61107/09_2025/9j36_61107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j36_61107/09_2025/9j36_61107.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.099 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: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 11008 2.51 5 N 2840 2.21 5 O 3012 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 116 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16960 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4240 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 19, 'TRANS': 503} Chain breaks: 1 Chain: "C" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4240 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 19, 'TRANS': 503} Chain breaks: 1 Chain: "D" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4240 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 19, 'TRANS': 503} Chain breaks: 1 Chain: "B" Number of atoms: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4240 Classifications: {'peptide': 523} Link IDs: {'PTRANS': 19, 'TRANS': 503} Chain breaks: 1 Time building chain proxies: 3.47, per 1000 atoms: 0.20 Number of scatterers: 16960 At special positions: 0 Unit cell: (112.772, 112.772, 137.004, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 3012 8.00 N 2840 7.00 C 11008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 310 " distance=2.04 Simple disulfide: pdb=" SG CYS A 292 " - pdb=" SG CYS A 333 " distance=2.04 Simple disulfide: pdb=" SG CYS A 297 " - pdb=" SG CYS A 303 " distance=2.03 Simple disulfide: pdb=" SG CYS C 129 " - pdb=" SG CYS C 310 " distance=2.04 Simple disulfide: pdb=" SG CYS C 292 " - pdb=" SG CYS C 333 " distance=2.04 Simple disulfide: pdb=" SG CYS C 297 " - pdb=" SG CYS C 303 " distance=2.03 Simple disulfide: pdb=" SG CYS D 129 " - pdb=" SG CYS D 310 " distance=2.04 Simple disulfide: pdb=" SG CYS D 292 " - pdb=" SG CYS D 333 " distance=2.04 Simple disulfide: pdb=" SG CYS D 297 " - pdb=" SG CYS D 303 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 310 " distance=2.04 Simple disulfide: pdb=" SG CYS B 292 " - pdb=" SG CYS B 333 " distance=2.04 Simple disulfide: pdb=" SG CYS B 297 " - pdb=" SG CYS B 303 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.00 Conformation dependent library (CDL) restraints added in 593.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4000 Finding SS restraints... Secondary structure from input PDB file: 107 helices and 20 sheets defined 61.4% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 103 through 111 removed outlier: 4.044A pdb=" N VAL A 111 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 119 removed outlier: 3.571A pdb=" N PHE A 117 " --> pdb=" O ASP A 114 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR A 119 " --> pdb=" O PHE A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 152 removed outlier: 5.029A pdb=" N THR A 139 " --> pdb=" O LYS A 135 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A 147 " --> pdb=" O LEU A 143 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE A 150 " --> pdb=" O PHE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 188 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 201 through 212 removed outlier: 3.641A pdb=" N VAL A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL A 207 " --> pdb=" O PRO A 203 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG A 209 " --> pdb=" O ILE A 205 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE A 210 " --> pdb=" O VAL A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 225 Processing helix chain 'A' and resid 226 through 240 removed outlier: 4.522A pdb=" N ILE A 235 " --> pdb=" O LEU A 231 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 262 through 267 removed outlier: 3.882A pdb=" N TYR A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 301 removed outlier: 3.527A pdb=" N ALA A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE A 298 " --> pdb=" O GLN A 294 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY A 301 " --> pdb=" O CYS A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 309 removed outlier: 3.502A pdb=" N LEU A 308 " --> pdb=" O THR A 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR A 309 " --> pdb=" O ASP A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 323 removed outlier: 3.825A pdb=" N ARG A 323 " --> pdb=" O ALA A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 334 removed outlier: 5.419A pdb=" N LYS A 330 " --> pdb=" O GLU A 326 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 355 removed outlier: 3.515A pdb=" N LEU A 353 " --> pdb=" O TYR A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 362 through 380 Processing helix chain 'A' and resid 390 through 423 Processing helix chain 'A' and resid 423 through 444 Processing helix chain 'A' and resid 446 through 465 Processing helix chain 'A' and resid 468 through 475 Processing helix chain 'A' and resid 477 through 494 removed outlier: 3.600A pdb=" N LEU A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ALA A 491 " --> pdb=" O HIS A 487 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL A 493 " --> pdb=" O CYS A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 removed outlier: 3.980A pdb=" N SER A 501 " --> pdb=" O PRO A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 511 Processing helix chain 'A' and resid 568 through 577 removed outlier: 3.824A pdb=" N LEU A 572 " --> pdb=" O GLY A 568 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THR A 573 " --> pdb=" O GLU A 569 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP A 574 " --> pdb=" O GLU A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 612 removed outlier: 3.798A pdb=" N PHE A 609 " --> pdb=" O GLU A 605 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL A 610 " --> pdb=" O GLU A 606 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 99 Processing helix chain 'C' and resid 103 through 111 removed outlier: 4.044A pdb=" N VAL C 111 " --> pdb=" O CYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 119 removed outlier: 3.572A pdb=" N PHE C 117 " --> pdb=" O ASP C 114 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR C 119 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 152 removed outlier: 5.029A pdb=" N THR C 139 " --> pdb=" O LYS C 135 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE C 147 " --> pdb=" O LEU C 143 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE C 150 " --> pdb=" O PHE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 188 Processing helix chain 'C' and resid 192 through 197 Processing helix chain 'C' and resid 201 through 212 removed outlier: 3.640A pdb=" N VAL C 206 " --> pdb=" O LEU C 202 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL C 207 " --> pdb=" O PRO C 203 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG C 209 " --> pdb=" O ILE C 205 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 217 No H-bonds generated for 'chain 'C' and resid 215 through 217' Processing helix chain 'C' and resid 218 through 225 Processing helix chain 'C' and resid 226 through 240 removed outlier: 4.523A pdb=" N ILE C 235 " --> pdb=" O LEU C 231 " (cutoff:3.500A) Proline residue: C 236 - end of helix Processing helix chain 'C' and resid 262 through 267 removed outlier: 3.881A pdb=" N TYR C 266 " --> pdb=" O GLY C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 301 removed outlier: 3.527A pdb=" N ALA C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE C 298 " --> pdb=" O GLN C 294 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP C 299 " --> pdb=" O GLU C 295 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA C 300 " --> pdb=" O ALA C 296 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY C 301 " --> pdb=" O CYS C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 309 removed outlier: 3.502A pdb=" N LEU C 308 " --> pdb=" O THR C 305 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR C 309 " --> pdb=" O ASP C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 323 removed outlier: 3.825A pdb=" N ARG C 323 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 334 removed outlier: 5.419A pdb=" N LYS C 330 " --> pdb=" O GLU C 326 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG C 334 " --> pdb=" O LYS C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 349 through 355 removed outlier: 3.516A pdb=" N LEU C 353 " --> pdb=" O TYR C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 360 Processing helix chain 'C' and resid 362 through 380 Processing helix chain 'C' and resid 390 through 423 Processing helix chain 'C' and resid 423 through 444 Processing helix chain 'C' and resid 446 through 465 Processing helix chain 'C' and resid 468 through 475 Processing helix chain 'C' and resid 477 through 494 removed outlier: 3.599A pdb=" N LEU C 490 " --> pdb=" O ARG C 486 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ALA C 491 " --> pdb=" O HIS C 487 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL C 493 " --> pdb=" O CYS C 489 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 501 removed outlier: 3.980A pdb=" N SER C 501 " --> pdb=" O PRO C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 511 Processing helix chain 'C' and resid 568 through 577 removed outlier: 3.823A pdb=" N LEU C 572 " --> pdb=" O GLY C 568 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR C 573 " --> pdb=" O GLU C 569 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP C 574 " --> pdb=" O GLU C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 612 removed outlier: 3.798A pdb=" N PHE C 609 " --> pdb=" O GLU C 605 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL C 610 " --> pdb=" O GLU C 606 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 99 Processing helix chain 'D' and resid 103 through 111 removed outlier: 4.044A pdb=" N VAL D 111 " --> pdb=" O CYS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 119 removed outlier: 3.572A pdb=" N PHE D 117 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR D 119 " --> pdb=" O PHE D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 152 removed outlier: 5.030A pdb=" N THR D 139 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE D 147 " --> pdb=" O LEU D 143 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE D 150 " --> pdb=" O PHE D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 188 Processing helix chain 'D' and resid 192 through 197 Processing helix chain 'D' and resid 201 through 212 removed outlier: 3.642A pdb=" N VAL D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N VAL D 207 " --> pdb=" O PRO D 203 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG D 209 " --> pdb=" O ILE D 205 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE D 210 " --> pdb=" O VAL D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 217 No H-bonds generated for 'chain 'D' and resid 215 through 217' Processing helix chain 'D' and resid 218 through 225 Processing helix chain 'D' and resid 226 through 240 removed outlier: 4.523A pdb=" N ILE D 235 " --> pdb=" O LEU D 231 " (cutoff:3.500A) Proline residue: D 236 - end of helix Processing helix chain 'D' and resid 262 through 267 removed outlier: 3.882A pdb=" N TYR D 266 " --> pdb=" O GLY D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 301 removed outlier: 3.527A pdb=" N ALA D 279 " --> pdb=" O HIS D 275 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE D 298 " --> pdb=" O GLN D 294 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASP D 299 " --> pdb=" O GLU D 295 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY D 301 " --> pdb=" O CYS D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 309 removed outlier: 3.502A pdb=" N LEU D 308 " --> pdb=" O THR D 305 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR D 309 " --> pdb=" O ASP D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 323 removed outlier: 3.825A pdb=" N ARG D 323 " --> pdb=" O ALA D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 334 removed outlier: 5.418A pdb=" N LYS D 330 " --> pdb=" O GLU D 326 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG D 334 " --> pdb=" O LYS D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 349 through 355 removed outlier: 3.515A pdb=" N LEU D 353 " --> pdb=" O TYR D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 360 Processing helix chain 'D' and resid 362 through 380 Processing helix chain 'D' and resid 390 through 423 Processing helix chain 'D' and resid 423 through 444 Processing helix chain 'D' and resid 446 through 465 Processing helix chain 'D' and resid 468 through 475 Processing helix chain 'D' and resid 477 through 494 removed outlier: 3.600A pdb=" N LEU D 490 " --> pdb=" O ARG D 486 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ALA D 491 " --> pdb=" O HIS D 487 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N LEU D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL D 493 " --> pdb=" O CYS D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 501 removed outlier: 3.981A pdb=" N SER D 501 " --> pdb=" O PRO D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 511 Processing helix chain 'D' and resid 568 through 577 removed outlier: 3.822A pdb=" N LEU D 572 " --> pdb=" O GLY D 568 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR D 573 " --> pdb=" O GLU D 569 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP D 574 " --> pdb=" O GLU D 570 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 612 removed outlier: 3.798A pdb=" N PHE D 609 " --> pdb=" O GLU D 605 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL D 610 " --> pdb=" O GLU D 606 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 103 through 111 removed outlier: 4.044A pdb=" N VAL B 111 " --> pdb=" O CYS B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 119 removed outlier: 3.572A pdb=" N PHE B 117 " --> pdb=" O ASP B 114 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR B 119 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 152 removed outlier: 5.030A pdb=" N THR B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE B 147 " --> pdb=" O LEU B 143 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE B 150 " --> pdb=" O PHE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 188 Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 201 through 212 removed outlier: 3.641A pdb=" N VAL B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL B 207 " --> pdb=" O PRO B 203 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ARG B 209 " --> pdb=" O ILE B 205 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N PHE B 210 " --> pdb=" O VAL B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 215 through 217 No H-bonds generated for 'chain 'B' and resid 215 through 217' Processing helix chain 'B' and resid 218 through 225 Processing helix chain 'B' and resid 226 through 240 removed outlier: 4.522A pdb=" N ILE B 235 " --> pdb=" O LEU B 231 " (cutoff:3.500A) Proline residue: B 236 - end of helix Processing helix chain 'B' and resid 262 through 267 removed outlier: 3.882A pdb=" N TYR B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 301 removed outlier: 3.527A pdb=" N ALA B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE B 298 " --> pdb=" O GLN B 294 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASP B 299 " --> pdb=" O GLU B 295 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 300 " --> pdb=" O ALA B 296 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY B 301 " --> pdb=" O CYS B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 309 removed outlier: 3.502A pdb=" N LEU B 308 " --> pdb=" O THR B 305 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 309 " --> pdb=" O ASP B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 317 through 323 removed outlier: 3.825A pdb=" N ARG B 323 " --> pdb=" O ALA B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 334 removed outlier: 5.419A pdb=" N LYS B 330 " --> pdb=" O GLU B 326 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 334 " --> pdb=" O LYS B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 355 removed outlier: 3.515A pdb=" N LEU B 353 " --> pdb=" O TYR B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 362 through 380 Processing helix chain 'B' and resid 390 through 423 Processing helix chain 'B' and resid 423 through 444 Processing helix chain 'B' and resid 446 through 465 Processing helix chain 'B' and resid 468 through 475 Processing helix chain 'B' and resid 477 through 494 removed outlier: 3.600A pdb=" N LEU B 490 " --> pdb=" O ARG B 486 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ALA B 491 " --> pdb=" O HIS B 487 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N LEU B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL B 493 " --> pdb=" O CYS B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 removed outlier: 3.980A pdb=" N SER B 501 " --> pdb=" O PRO B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 511 Processing helix chain 'B' and resid 568 through 577 removed outlier: 3.824A pdb=" N LEU B 572 " --> pdb=" O GLY B 568 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR B 573 " --> pdb=" O GLU B 569 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP B 574 " --> pdb=" O GLU B 570 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 612 removed outlier: 3.797A pdb=" N PHE B 609 " --> pdb=" O GLU B 605 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL B 610 " --> pdb=" O GLU B 606 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 124 Processing sheet with id=AA2, first strand: chain 'A' and resid 164 through 165 Processing sheet with id=AA3, first strand: chain 'A' and resid 515 through 519 removed outlier: 6.428A pdb=" N GLU A 598 " --> pdb=" O ILE A 539 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.716A pdb=" N VAL A 591 " --> pdb=" O LEU A 525 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 543 through 545 removed outlier: 3.616A pdb=" N LEU A 561 " --> pdb=" O LEU A 543 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 121 through 124 Processing sheet with id=AA7, first strand: chain 'C' and resid 164 through 165 Processing sheet with id=AA8, first strand: chain 'C' and resid 515 through 519 removed outlier: 6.428A pdb=" N GLU C 598 " --> pdb=" O ILE C 539 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 524 through 526 removed outlier: 6.716A pdb=" N VAL C 591 " --> pdb=" O LEU C 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 543 through 545 removed outlier: 3.616A pdb=" N LEU C 561 " --> pdb=" O LEU C 543 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 121 through 124 Processing sheet with id=AB3, first strand: chain 'D' and resid 164 through 165 Processing sheet with id=AB4, first strand: chain 'D' and resid 515 through 519 removed outlier: 6.427A pdb=" N GLU D 598 " --> pdb=" O ILE D 539 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 524 through 526 removed outlier: 6.715A pdb=" N VAL D 591 " --> pdb=" O LEU D 525 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 543 through 545 removed outlier: 3.617A pdb=" N LEU D 561 " --> pdb=" O LEU D 543 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 121 through 124 Processing sheet with id=AB8, first strand: chain 'B' and resid 164 through 165 Processing sheet with id=AB9, first strand: chain 'B' and resid 515 through 519 removed outlier: 6.427A pdb=" N GLU B 598 " --> pdb=" O ILE B 539 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 524 through 526 removed outlier: 6.716A pdb=" N VAL B 591 " --> pdb=" O LEU B 525 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 543 through 545 removed outlier: 3.615A pdb=" N LEU B 561 " --> pdb=" O LEU B 543 " (cutoff:3.500A) 820 hydrogen bonds defined for protein. 2328 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.53 Time building geometry restraints manager: 1.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2699 1.29 - 1.42: 4651 1.42 - 1.55: 9833 1.55 - 1.68: 21 1.68 - 1.81: 144 Bond restraints: 17348 Sorted by residual: bond pdb=" C GLY D 384 " pdb=" N LEU D 385 " ideal model delta sigma weight residual 1.330 1.207 0.123 1.41e-02 5.03e+03 7.63e+01 bond pdb=" C GLY A 384 " pdb=" N LEU A 385 " ideal model delta sigma weight residual 1.330 1.209 0.121 1.41e-02 5.03e+03 7.42e+01 bond pdb=" C SER A 217 " pdb=" N ASP A 218 " ideal model delta sigma weight residual 1.333 1.220 0.114 1.34e-02 5.57e+03 7.19e+01 bond pdb=" C GLY B 384 " pdb=" N LEU B 385 " ideal model delta sigma weight residual 1.330 1.216 0.114 1.41e-02 5.03e+03 6.53e+01 bond pdb=" CA GLN A 383 " pdb=" C GLN A 383 " ideal model delta sigma weight residual 1.523 1.422 0.101 1.35e-02 5.49e+03 5.62e+01 ... (remaining 17343 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.24: 23326 5.24 - 10.47: 152 10.47 - 15.71: 14 15.71 - 20.94: 15 20.94 - 26.18: 1 Bond angle restraints: 23508 Sorted by residual: angle pdb=" C GLY C 384 " pdb=" N LEU C 385 " pdb=" CA LEU C 385 " ideal model delta sigma weight residual 121.02 147.20 -26.18 1.48e+00 4.57e-01 3.13e+02 angle pdb=" O GLY C 384 " pdb=" C GLY C 384 " pdb=" N LEU C 385 " ideal model delta sigma weight residual 122.70 103.83 18.87 1.30e+00 5.92e-01 2.11e+02 angle pdb=" N GLN D 158 " pdb=" CA GLN D 158 " pdb=" C GLN D 158 " ideal model delta sigma weight residual 113.16 96.94 16.22 1.24e+00 6.50e-01 1.71e+02 angle pdb=" N GLN B 158 " pdb=" CA GLN B 158 " pdb=" C GLN B 158 " ideal model delta sigma weight residual 113.16 96.97 16.19 1.24e+00 6.50e-01 1.71e+02 angle pdb=" C GLY A 384 " pdb=" N LEU A 385 " pdb=" CA LEU A 385 " ideal model delta sigma weight residual 122.30 139.37 -17.07 1.35e+00 5.49e-01 1.60e+02 ... (remaining 23503 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 9147 17.15 - 34.30: 1042 34.30 - 51.45: 159 51.45 - 68.60: 40 68.60 - 85.75: 20 Dihedral angle restraints: 10408 sinusoidal: 4240 harmonic: 6168 Sorted by residual: dihedral pdb=" C SER B 217 " pdb=" N SER B 217 " pdb=" CA SER B 217 " pdb=" CB SER B 217 " ideal model delta harmonic sigma weight residual -122.60 -147.30 24.70 0 2.50e+00 1.60e-01 9.76e+01 dihedral pdb=" C SER C 217 " pdb=" N SER C 217 " pdb=" CA SER C 217 " pdb=" CB SER C 217 " ideal model delta harmonic sigma weight residual -122.60 -145.52 22.92 0 2.50e+00 1.60e-01 8.40e+01 dihedral pdb=" C SER D 217 " pdb=" N SER D 217 " pdb=" CA SER D 217 " pdb=" CB SER D 217 " ideal model delta harmonic sigma weight residual -122.60 -145.51 22.91 0 2.50e+00 1.60e-01 8.40e+01 ... (remaining 10405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.196: 2631 0.196 - 0.392: 9 0.392 - 0.589: 5 0.589 - 0.785: 1 0.785 - 0.981: 6 Chirality restraints: 2652 Sorted by residual: chirality pdb=" CA SER B 217 " pdb=" N SER B 217 " pdb=" C SER B 217 " pdb=" CB SER B 217 " both_signs ideal model delta sigma weight residual False 2.51 1.53 0.98 2.00e-01 2.50e+01 2.41e+01 chirality pdb=" CA SER D 217 " pdb=" N SER D 217 " pdb=" C SER D 217 " pdb=" CB SER D 217 " both_signs ideal model delta sigma weight residual False 2.51 1.59 0.92 2.00e-01 2.50e+01 2.10e+01 chirality pdb=" CA SER C 217 " pdb=" N SER C 217 " pdb=" C SER C 217 " pdb=" CB SER C 217 " both_signs ideal model delta sigma weight residual False 2.51 1.60 0.91 2.00e-01 2.50e+01 2.09e+01 ... (remaining 2649 not shown) Planarity restraints: 2948 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 217 " 0.032 2.00e-02 2.50e+03 5.94e-02 3.53e+01 pdb=" C SER A 217 " -0.103 2.00e-02 2.50e+03 pdb=" O SER A 217 " 0.034 2.00e-02 2.50e+03 pdb=" N ASP A 218 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 384 " -0.023 2.00e-02 2.50e+03 3.63e-02 1.32e+01 pdb=" C GLY C 384 " 0.063 2.00e-02 2.50e+03 pdb=" O GLY C 384 " -0.019 2.00e-02 2.50e+03 pdb=" N LEU C 385 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 114 " -0.044 5.00e-02 4.00e+02 6.58e-02 6.92e+00 pdb=" N PRO D 115 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO D 115 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 115 " -0.037 5.00e-02 4.00e+02 ... (remaining 2945 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 170 2.61 - 3.18: 13237 3.18 - 3.75: 26666 3.75 - 4.33: 37546 4.33 - 4.90: 61646 Nonbonded interactions: 139265 Sorted by model distance: nonbonded pdb=" O MET C 155 " pdb=" CG LEU C 159 " model vdw 2.036 3.470 nonbonded pdb=" OE1 GLN B 158 " pdb=" CE1 TYR B 187 " model vdw 2.144 3.340 nonbonded pdb=" OE1 GLN B 158 " pdb=" OH TYR B 187 " model vdw 2.147 3.040 nonbonded pdb=" OE1 GLN D 158 " pdb=" OH TYR D 187 " model vdw 2.151 3.040 nonbonded pdb=" OE1 GLN D 158 " pdb=" CE1 TYR D 187 " model vdw 2.154 3.340 ... (remaining 139260 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 3.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.470 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:7.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 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 : 0.010 0.123 17360 Z= 0.530 Angle : 1.295 26.179 23532 Z= 0.797 Chirality : 0.076 0.981 2652 Planarity : 0.006 0.066 2948 Dihedral : 15.083 85.752 6372 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.60 % Favored : 93.40 % Rotamer: Outliers : 0.86 % Allowed : 9.40 % Favored : 89.74 % Cbeta Deviations : 0.55 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.35 (0.14), residues: 2076 helix: -3.01 (0.11), residues: 1232 sheet: -2.73 (0.38), residues: 88 loop : -2.31 (0.19), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 433 TYR 0.021 0.004 TYR C 270 PHE 0.020 0.003 PHE C 363 TRP 0.013 0.002 TRP B 372 HIS 0.006 0.002 HIS C 154 Details of bonding type rmsd covalent geometry : bond 0.01018 (17348) covalent geometry : angle 1.29335 (23508) SS BOND : bond 0.00633 ( 12) SS BOND : angle 2.48401 ( 24) hydrogen bonds : bond 0.22079 ( 820) hydrogen bonds : angle 8.65320 ( 2328) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 238 time to evaluate : 0.539 Fit side-chains REVERT: A 232 VAL cc_start: 0.6463 (m) cc_final: 0.6221 (p) REVERT: A 429 MET cc_start: 0.8110 (tmm) cc_final: 0.7862 (tmt) REVERT: A 508 ASP cc_start: 0.6799 (m-30) cc_final: 0.6419 (p0) REVERT: A 540 ARG cc_start: 0.7612 (ttp-170) cc_final: 0.7401 (ttp80) REVERT: C 313 GLN cc_start: 0.6471 (mp10) cc_final: 0.6169 (mp10) REVERT: C 429 MET cc_start: 0.8162 (tmm) cc_final: 0.7822 (tmt) REVERT: C 522 SER cc_start: 0.8125 (m) cc_final: 0.7908 (p) REVERT: D 232 VAL cc_start: 0.6437 (m) cc_final: 0.6203 (p) REVERT: D 429 MET cc_start: 0.8100 (tmm) cc_final: 0.7888 (tmt) REVERT: D 508 ASP cc_start: 0.6788 (m-30) cc_final: 0.6416 (p0) REVERT: D 540 ARG cc_start: 0.7588 (ttp-170) cc_final: 0.7337 (ttp80) REVERT: B 232 VAL cc_start: 0.6422 (m) cc_final: 0.6180 (p) REVERT: B 429 MET cc_start: 0.8114 (tmm) cc_final: 0.7894 (tmt) REVERT: B 508 ASP cc_start: 0.6754 (m-30) cc_final: 0.6410 (p0) REVERT: B 540 ARG cc_start: 0.7611 (ttp-170) cc_final: 0.7331 (ttp80) outliers start: 16 outliers final: 8 residues processed: 250 average time/residue: 0.5085 time to fit residues: 142.4835 Evaluate side-chains 166 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 158 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 501 SER Chi-restraints excluded: chain C residue 381 LEU Chi-restraints excluded: chain C residue 501 SER Chi-restraints excluded: chain D residue 381 LEU Chi-restraints excluded: chain D residue 501 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 501 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 0.2980 chunk 122 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 HIS A 340 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN C 154 HIS C 340 ASN ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 414 ASN D 154 HIS D 340 ASN ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN B 154 HIS B 340 ASN ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.218411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.150430 restraints weight = 17768.459| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.33 r_work: 0.3841 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3717 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17360 Z= 0.130 Angle : 0.602 8.103 23532 Z= 0.320 Chirality : 0.040 0.150 2652 Planarity : 0.004 0.039 2948 Dihedral : 5.918 33.280 2320 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.70 % Allowed : 13.17 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.37 (0.17), residues: 2076 helix: -1.30 (0.14), residues: 1276 sheet: -1.64 (0.42), residues: 88 loop : -1.79 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 589 TYR 0.014 0.002 TYR D 270 PHE 0.014 0.001 PHE C 363 TRP 0.010 0.001 TRP D 574 HIS 0.004 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00297 (17348) covalent geometry : angle 0.60188 (23508) SS BOND : bond 0.00140 ( 12) SS BOND : angle 0.80478 ( 24) hydrogen bonds : bond 0.03700 ( 820) hydrogen bonds : angle 4.92354 ( 2328) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 189 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.6163 (mpp) cc_final: 0.5351 (mpp) REVERT: A 392 MET cc_start: 0.8188 (ttt) cc_final: 0.7591 (tmt) REVERT: A 429 MET cc_start: 0.8490 (tmm) cc_final: 0.8175 (tmt) REVERT: A 486 ARG cc_start: 0.7349 (mtt90) cc_final: 0.6802 (mtt90) REVERT: A 540 ARG cc_start: 0.7434 (ttp-170) cc_final: 0.7066 (ttp80) REVERT: A 565 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6869 (mt-10) REVERT: C 155 MET cc_start: 0.5507 (mpp) cc_final: 0.4996 (mpp) REVERT: C 214 SER cc_start: 0.4166 (OUTLIER) cc_final: 0.3718 (t) REVERT: C 287 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7070 (tm-30) REVERT: C 313 GLN cc_start: 0.6297 (mp10) cc_final: 0.5931 (mp10) REVERT: C 330 LYS cc_start: 0.8028 (OUTLIER) cc_final: 0.6954 (tppt) REVERT: C 336 ASP cc_start: 0.8110 (m-30) cc_final: 0.7852 (m-30) REVERT: C 415 MET cc_start: 0.8112 (tpp) cc_final: 0.7671 (mtt) REVERT: C 429 MET cc_start: 0.8520 (tmm) cc_final: 0.8208 (tmt) REVERT: C 486 ARG cc_start: 0.7262 (mtt90) cc_final: 0.6903 (mtt90) REVERT: C 562 LYS cc_start: 0.7256 (mptt) cc_final: 0.6006 (pttm) REVERT: C 565 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7030 (mt-10) REVERT: D 155 MET cc_start: 0.6073 (mpp) cc_final: 0.5366 (mpp) REVERT: D 392 MET cc_start: 0.8147 (ttt) cc_final: 0.7569 (tmt) REVERT: D 415 MET cc_start: 0.8179 (tpp) cc_final: 0.7766 (mtt) REVERT: D 429 MET cc_start: 0.8520 (tmm) cc_final: 0.8148 (tmt) REVERT: D 486 ARG cc_start: 0.7328 (mtt90) cc_final: 0.7047 (mtt90) REVERT: D 508 ASP cc_start: 0.6701 (m-30) cc_final: 0.6262 (p0) REVERT: D 540 ARG cc_start: 0.7480 (ttp-170) cc_final: 0.7206 (ttp80) REVERT: D 562 LYS cc_start: 0.7012 (OUTLIER) cc_final: 0.5791 (pttm) REVERT: D 565 GLU cc_start: 0.7248 (mt-10) cc_final: 0.7014 (mt-10) REVERT: B 155 MET cc_start: 0.5906 (mpp) cc_final: 0.5120 (mpp) REVERT: B 415 MET cc_start: 0.8156 (tpp) cc_final: 0.7794 (mtt) REVERT: B 429 MET cc_start: 0.8520 (tmm) cc_final: 0.8153 (tmt) REVERT: B 486 ARG cc_start: 0.7393 (mtt90) cc_final: 0.7091 (mtt90) REVERT: B 508 ASP cc_start: 0.6649 (m-30) cc_final: 0.6283 (p0) REVERT: B 535 MET cc_start: 0.7932 (ttm) cc_final: 0.7677 (ttp) REVERT: B 540 ARG cc_start: 0.7367 (ttp-170) cc_final: 0.7107 (ttp80) REVERT: B 562 LYS cc_start: 0.6968 (OUTLIER) cc_final: 0.6737 (mptt) REVERT: B 565 GLU cc_start: 0.7219 (mt-10) cc_final: 0.6945 (mt-10) outliers start: 50 outliers final: 19 residues processed: 221 average time/residue: 0.4923 time to fit residues: 122.6833 Evaluate side-chains 182 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain C residue 214 SER Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 562 LYS Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 595 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 60 optimal weight: 0.0970 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 195 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 205 optimal weight: 0.4980 chunk 148 optimal weight: 0.4980 chunk 117 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.218819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.150409 restraints weight = 17883.017| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.36 r_work: 0.3870 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17360 Z= 0.114 Angle : 0.560 8.209 23532 Z= 0.292 Chirality : 0.039 0.158 2652 Planarity : 0.004 0.054 2948 Dihedral : 5.301 30.428 2308 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.21 % Allowed : 14.79 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.46 (0.18), residues: 2076 helix: -0.41 (0.15), residues: 1260 sheet: -0.78 (0.45), residues: 88 loop : -1.84 (0.20), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 486 TYR 0.014 0.002 TYR B 266 PHE 0.012 0.001 PHE B 363 TRP 0.010 0.001 TRP D 574 HIS 0.004 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00258 (17348) covalent geometry : angle 0.55944 (23508) SS BOND : bond 0.00098 ( 12) SS BOND : angle 0.71883 ( 24) hydrogen bonds : bond 0.03108 ( 820) hydrogen bonds : angle 4.47418 ( 2328) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 171 time to evaluate : 0.697 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.5887 (mpp) cc_final: 0.5160 (mpp) REVERT: A 214 SER cc_start: 0.4152 (OUTLIER) cc_final: 0.3896 (t) REVERT: A 287 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7153 (mm-30) REVERT: A 415 MET cc_start: 0.8220 (mtp) cc_final: 0.7652 (mtt) REVERT: A 419 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8188 (mp) REVERT: A 429 MET cc_start: 0.8615 (tmm) cc_final: 0.8219 (tmt) REVERT: A 486 ARG cc_start: 0.7195 (mtt90) cc_final: 0.6866 (mtt90) REVERT: A 540 ARG cc_start: 0.7443 (ttp-170) cc_final: 0.7222 (ttp80) REVERT: A 565 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6845 (mt-10) REVERT: A 594 LEU cc_start: 0.8493 (mt) cc_final: 0.8270 (mt) REVERT: A 595 THR cc_start: 0.8246 (OUTLIER) cc_final: 0.7858 (p) REVERT: C 155 MET cc_start: 0.5408 (mpp) cc_final: 0.4607 (mpp) REVERT: C 287 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7139 (tm-30) REVERT: C 313 GLN cc_start: 0.6567 (mp10) cc_final: 0.6031 (mp10) REVERT: C 315 MET cc_start: 0.7064 (mtp) cc_final: 0.6688 (mtm) REVERT: C 330 LYS cc_start: 0.8019 (OUTLIER) cc_final: 0.7039 (tppt) REVERT: C 336 ASP cc_start: 0.8126 (m-30) cc_final: 0.7794 (m-30) REVERT: C 392 MET cc_start: 0.7978 (tpt) cc_final: 0.7357 (ttt) REVERT: C 415 MET cc_start: 0.8232 (tpp) cc_final: 0.7755 (mtt) REVERT: C 429 MET cc_start: 0.8617 (tmm) cc_final: 0.8289 (tmt) REVERT: C 486 ARG cc_start: 0.7377 (mtt90) cc_final: 0.6909 (mtt90) REVERT: C 565 GLU cc_start: 0.7309 (mt-10) cc_final: 0.6885 (mt-10) REVERT: D 155 MET cc_start: 0.5831 (mpp) cc_final: 0.5244 (mpp) REVERT: D 287 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7144 (mm-30) REVERT: D 415 MET cc_start: 0.8231 (tpp) cc_final: 0.7801 (mtt) REVERT: D 429 MET cc_start: 0.8615 (tmm) cc_final: 0.8223 (tmt) REVERT: D 486 ARG cc_start: 0.7490 (mtt90) cc_final: 0.7180 (mtt90) REVERT: D 508 ASP cc_start: 0.6672 (m-30) cc_final: 0.6133 (p0) REVERT: D 540 ARG cc_start: 0.7480 (ttp-170) cc_final: 0.7135 (ttp80) REVERT: D 562 LYS cc_start: 0.7067 (OUTLIER) cc_final: 0.5802 (pttm) REVERT: D 565 GLU cc_start: 0.7316 (mt-10) cc_final: 0.6992 (mt-10) REVERT: D 594 LEU cc_start: 0.8498 (mt) cc_final: 0.8270 (mt) REVERT: B 155 MET cc_start: 0.5708 (mpp) cc_final: 0.5133 (mpp) REVERT: B 287 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7152 (mm-30) REVERT: B 415 MET cc_start: 0.8219 (tpp) cc_final: 0.7782 (mtt) REVERT: B 429 MET cc_start: 0.8627 (tmm) cc_final: 0.8243 (tmt) REVERT: B 486 ARG cc_start: 0.7499 (mtt90) cc_final: 0.7065 (mtt90) REVERT: B 562 LYS cc_start: 0.7011 (OUTLIER) cc_final: 0.5766 (pttm) REVERT: B 565 GLU cc_start: 0.7296 (mt-10) cc_final: 0.7058 (mt-10) REVERT: B 594 LEU cc_start: 0.8492 (mt) cc_final: 0.8276 (mt) REVERT: B 595 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.7851 (p) outliers start: 41 outliers final: 14 residues processed: 194 average time/residue: 0.5812 time to fit residues: 126.5159 Evaluate side-chains 170 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 562 LYS Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 595 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 60 optimal weight: 6.9990 chunk 87 optimal weight: 0.9990 chunk 110 optimal weight: 5.9990 chunk 193 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 143 optimal weight: 0.0060 chunk 207 optimal weight: 6.9990 chunk 190 optimal weight: 1.9990 overall best weight: 1.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 124 ASN ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.215847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.145299 restraints weight = 17444.051| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.32 r_work: 0.3811 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3694 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17360 Z= 0.190 Angle : 0.608 7.087 23532 Z= 0.317 Chirality : 0.042 0.163 2652 Planarity : 0.004 0.045 2948 Dihedral : 5.329 31.974 2308 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 2.97 % Allowed : 15.44 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.41 (0.18), residues: 2076 helix: -0.33 (0.15), residues: 1284 sheet: -0.42 (0.48), residues: 88 loop : -2.01 (0.20), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 542 TYR 0.015 0.002 TYR D 367 PHE 0.021 0.002 PHE C 103 TRP 0.009 0.001 TRP D 574 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00450 (17348) covalent geometry : angle 0.60709 (23508) SS BOND : bond 0.00225 ( 12) SS BOND : angle 0.99868 ( 24) hydrogen bonds : bond 0.03611 ( 820) hydrogen bonds : angle 4.64418 ( 2328) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 169 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.5614 (mpp) cc_final: 0.4908 (mpp) REVERT: A 214 SER cc_start: 0.4230 (OUTLIER) cc_final: 0.3967 (t) REVERT: A 287 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7231 (mm-30) REVERT: A 419 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.8139 (mp) REVERT: A 429 MET cc_start: 0.8607 (tmm) cc_final: 0.8302 (tmt) REVERT: A 486 ARG cc_start: 0.7370 (mtt90) cc_final: 0.6965 (mtt90) REVERT: A 540 ARG cc_start: 0.7657 (ttp-170) cc_final: 0.7200 (ttp80) REVERT: A 544 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6343 (tp30) REVERT: A 565 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6852 (mt-10) REVERT: C 155 MET cc_start: 0.5281 (mpp) cc_final: 0.4465 (mpp) REVERT: C 232 VAL cc_start: 0.6287 (m) cc_final: 0.5979 (p) REVERT: C 287 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7055 (tm-30) REVERT: C 330 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7134 (tppt) REVERT: C 392 MET cc_start: 0.8054 (tpt) cc_final: 0.7438 (ttt) REVERT: C 486 ARG cc_start: 0.7584 (mtt90) cc_final: 0.7036 (mtt90) REVERT: C 544 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6279 (tp30) REVERT: C 565 GLU cc_start: 0.7312 (mt-10) cc_final: 0.6883 (mt-10) REVERT: D 155 MET cc_start: 0.5713 (mpp) cc_final: 0.5075 (mpp) REVERT: D 287 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7228 (mm-30) REVERT: D 415 MET cc_start: 0.8215 (tpp) cc_final: 0.7944 (tpp) REVERT: D 429 MET cc_start: 0.8608 (tmm) cc_final: 0.8301 (tmt) REVERT: D 486 ARG cc_start: 0.7592 (mtt90) cc_final: 0.7125 (mtt90) REVERT: D 540 ARG cc_start: 0.7695 (ttp-170) cc_final: 0.7331 (ttp80) REVERT: D 544 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.6352 (tp30) REVERT: D 562 LYS cc_start: 0.7070 (OUTLIER) cc_final: 0.5820 (pttm) REVERT: D 565 GLU cc_start: 0.7348 (mt-10) cc_final: 0.7082 (mt-10) REVERT: B 155 MET cc_start: 0.5708 (mpp) cc_final: 0.5071 (mpp) REVERT: B 287 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7221 (mm-30) REVERT: B 429 MET cc_start: 0.8618 (tmm) cc_final: 0.8291 (tmt) REVERT: B 486 ARG cc_start: 0.7566 (mtt90) cc_final: 0.6941 (mtt90) REVERT: B 544 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.6350 (tp30) REVERT: B 562 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.5827 (pttm) REVERT: B 565 GLU cc_start: 0.7282 (mt-10) cc_final: 0.7051 (mt-10) outliers start: 55 outliers final: 22 residues processed: 202 average time/residue: 0.5353 time to fit residues: 121.6842 Evaluate side-chains 194 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 544 GLU Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 544 GLU Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 535 MET Chi-restraints excluded: chain D residue 544 GLU Chi-restraints excluded: chain D residue 562 LYS Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 544 GLU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 595 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 78 optimal weight: 1.9990 chunk 23 optimal weight: 0.1980 chunk 58 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 85 optimal weight: 2.9990 chunk 181 optimal weight: 0.5980 chunk 151 optimal weight: 9.9990 chunk 174 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.218091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.148205 restraints weight = 17456.179| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 2.32 r_work: 0.3839 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3722 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17360 Z= 0.113 Angle : 0.528 6.960 23532 Z= 0.278 Chirality : 0.039 0.157 2652 Planarity : 0.003 0.041 2948 Dihedral : 4.996 28.540 2308 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 2.97 % Allowed : 15.60 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.18), residues: 2076 helix: 0.06 (0.16), residues: 1276 sheet: 0.07 (0.49), residues: 88 loop : -1.88 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.013 0.001 TYR C 266 PHE 0.024 0.001 PHE B 103 TRP 0.006 0.001 TRP A 574 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00260 (17348) covalent geometry : angle 0.52827 (23508) SS BOND : bond 0.00110 ( 12) SS BOND : angle 0.70659 ( 24) hydrogen bonds : bond 0.02912 ( 820) hydrogen bonds : angle 4.29835 ( 2328) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 173 time to evaluate : 0.583 Fit side-chains REVERT: A 155 MET cc_start: 0.5518 (mpp) cc_final: 0.4912 (mpp) REVERT: A 214 SER cc_start: 0.4190 (OUTLIER) cc_final: 0.3946 (t) REVERT: A 287 GLU cc_start: 0.8025 (OUTLIER) cc_final: 0.7065 (mm-30) REVERT: A 419 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.8100 (mp) REVERT: A 429 MET cc_start: 0.8612 (tmm) cc_final: 0.8223 (tmt) REVERT: A 486 ARG cc_start: 0.7202 (mtt90) cc_final: 0.6811 (mtt90) REVERT: A 540 ARG cc_start: 0.7408 (ttp-170) cc_final: 0.6917 (ttp80) REVERT: A 565 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6835 (mt-10) REVERT: A 594 LEU cc_start: 0.8378 (mt) cc_final: 0.8157 (mt) REVERT: A 595 THR cc_start: 0.8171 (OUTLIER) cc_final: 0.7854 (p) REVERT: C 155 MET cc_start: 0.5306 (mpp) cc_final: 0.4676 (mpp) REVERT: C 232 VAL cc_start: 0.6342 (m) cc_final: 0.6049 (p) REVERT: C 287 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7085 (tm-30) REVERT: C 313 GLN cc_start: 0.6703 (mp10) cc_final: 0.6303 (mp10) REVERT: C 330 LYS cc_start: 0.8240 (OUTLIER) cc_final: 0.7245 (tppt) REVERT: C 392 MET cc_start: 0.7958 (tpt) cc_final: 0.7313 (ttt) REVERT: C 415 MET cc_start: 0.8132 (tpp) cc_final: 0.7739 (mtt) REVERT: C 429 MET cc_start: 0.8619 (tmm) cc_final: 0.8233 (tmt) REVERT: C 565 GLU cc_start: 0.7338 (mt-10) cc_final: 0.6833 (mt-10) REVERT: C 595 THR cc_start: 0.8160 (OUTLIER) cc_final: 0.7849 (p) REVERT: D 155 MET cc_start: 0.5524 (mpp) cc_final: 0.4918 (mpp) REVERT: D 287 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7071 (mm-30) REVERT: D 313 GLN cc_start: 0.6607 (mp10) cc_final: 0.6253 (mp10) REVERT: D 429 MET cc_start: 0.8604 (tmm) cc_final: 0.8214 (tmt) REVERT: D 486 ARG cc_start: 0.7477 (mtt90) cc_final: 0.7152 (mtt90) REVERT: D 508 ASP cc_start: 0.6586 (m-30) cc_final: 0.5740 (p0) REVERT: D 540 ARG cc_start: 0.7475 (ttp-170) cc_final: 0.7101 (ttp80) REVERT: D 562 LYS cc_start: 0.7058 (OUTLIER) cc_final: 0.6623 (mptt) REVERT: D 565 GLU cc_start: 0.7400 (mt-10) cc_final: 0.6955 (mt-10) REVERT: D 594 LEU cc_start: 0.8383 (mt) cc_final: 0.8163 (mt) REVERT: D 595 THR cc_start: 0.8175 (OUTLIER) cc_final: 0.7868 (p) REVERT: B 155 MET cc_start: 0.5499 (mpp) cc_final: 0.4907 (mpp) REVERT: B 287 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7035 (mm-30) REVERT: B 313 GLN cc_start: 0.6591 (mp10) cc_final: 0.6237 (mp10) REVERT: B 415 MET cc_start: 0.8135 (tpp) cc_final: 0.7785 (mtt) REVERT: B 429 MET cc_start: 0.8616 (tmm) cc_final: 0.8214 (tmt) REVERT: B 486 ARG cc_start: 0.7209 (mtt90) cc_final: 0.6850 (mtt90) REVERT: B 540 ARG cc_start: 0.7472 (ttp80) cc_final: 0.7046 (ttp80) REVERT: B 543 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7999 (mp) REVERT: B 562 LYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6592 (mptt) REVERT: B 565 GLU cc_start: 0.7292 (mt-10) cc_final: 0.6816 (mt-10) REVERT: B 594 LEU cc_start: 0.8336 (mt) cc_final: 0.8107 (mt) REVERT: B 595 THR cc_start: 0.8147 (OUTLIER) cc_final: 0.7833 (p) outliers start: 55 outliers final: 24 residues processed: 209 average time/residue: 0.6045 time to fit residues: 140.8723 Evaluate side-chains 203 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 165 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 SER Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 419 LEU Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain D residue 106 SER Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 562 LYS Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain B residue 106 SER Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 595 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 146 optimal weight: 0.1980 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 0.0370 chunk 154 optimal weight: 0.5980 chunk 55 optimal weight: 0.0770 chunk 166 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 420 GLN C 420 GLN ** D 289 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.220208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.150962 restraints weight = 17418.800| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.32 r_work: 0.3867 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.2981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17360 Z= 0.091 Angle : 0.500 6.977 23532 Z= 0.261 Chirality : 0.038 0.163 2652 Planarity : 0.003 0.044 2948 Dihedral : 4.704 27.989 2308 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.48 % Allowed : 16.63 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.19), residues: 2076 helix: 0.44 (0.16), residues: 1248 sheet: 0.36 (0.50), residues: 88 loop : -1.84 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 527 TYR 0.007 0.001 TYR B 309 PHE 0.023 0.001 PHE B 103 TRP 0.007 0.001 TRP A 281 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00203 (17348) covalent geometry : angle 0.49938 (23508) SS BOND : bond 0.00074 ( 12) SS BOND : angle 0.64060 ( 24) hydrogen bonds : bond 0.02573 ( 820) hydrogen bonds : angle 4.06942 ( 2328) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 0.609 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.5432 (mpp) cc_final: 0.4807 (mpp) REVERT: A 287 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7010 (mm-30) REVERT: A 313 GLN cc_start: 0.6696 (mp10) cc_final: 0.6259 (mp10) REVERT: A 314 ASN cc_start: 0.7883 (m-40) cc_final: 0.7592 (m-40) REVERT: A 415 MET cc_start: 0.8123 (mtp) cc_final: 0.7543 (mtt) REVERT: A 429 MET cc_start: 0.8567 (tmm) cc_final: 0.8177 (tmt) REVERT: A 486 ARG cc_start: 0.7129 (mtt90) cc_final: 0.6761 (mtt90) REVERT: A 540 ARG cc_start: 0.7336 (ttp-170) cc_final: 0.6984 (ttp80) REVERT: A 543 LEU cc_start: 0.8324 (mp) cc_final: 0.8113 (mm) REVERT: A 565 GLU cc_start: 0.7420 (mt-10) cc_final: 0.6979 (mt-10) REVERT: A 567 CYS cc_start: 0.6874 (OUTLIER) cc_final: 0.6077 (t) REVERT: A 594 LEU cc_start: 0.8394 (mt) cc_final: 0.8159 (mt) REVERT: A 595 THR cc_start: 0.8149 (OUTLIER) cc_final: 0.7915 (p) REVERT: C 155 MET cc_start: 0.5121 (mpp) cc_final: 0.4557 (mpp) REVERT: C 232 VAL cc_start: 0.6482 (m) cc_final: 0.6145 (p) REVERT: C 270 TYR cc_start: 0.8350 (OUTLIER) cc_final: 0.6381 (t80) REVERT: C 313 GLN cc_start: 0.6675 (mp10) cc_final: 0.6314 (mp10) REVERT: C 330 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7342 (tppt) REVERT: C 392 MET cc_start: 0.7912 (tpt) cc_final: 0.7286 (ttt) REVERT: C 429 MET cc_start: 0.8561 (tmm) cc_final: 0.8178 (tmt) REVERT: C 486 ARG cc_start: 0.7145 (ttm170) cc_final: 0.6643 (ttm110) REVERT: C 565 GLU cc_start: 0.7484 (mt-10) cc_final: 0.7005 (mt-10) REVERT: C 594 LEU cc_start: 0.8363 (mt) cc_final: 0.8146 (mt) REVERT: C 595 THR cc_start: 0.8199 (OUTLIER) cc_final: 0.7984 (p) REVERT: D 155 MET cc_start: 0.5367 (mpp) cc_final: 0.4798 (mpp) REVERT: D 287 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7029 (mm-30) REVERT: D 313 GLN cc_start: 0.6643 (mp10) cc_final: 0.6301 (mp10) REVERT: D 415 MET cc_start: 0.8106 (tpp) cc_final: 0.7785 (mtt) REVERT: D 429 MET cc_start: 0.8564 (tmm) cc_final: 0.8174 (tmt) REVERT: D 486 ARG cc_start: 0.7427 (mtt90) cc_final: 0.6958 (mtt90) REVERT: D 540 ARG cc_start: 0.7397 (ttp-170) cc_final: 0.7175 (ttp80) REVERT: D 565 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7110 (mt-10) REVERT: D 594 LEU cc_start: 0.8369 (mt) cc_final: 0.8115 (mt) REVERT: D 595 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7948 (p) REVERT: B 155 MET cc_start: 0.5333 (mpp) cc_final: 0.4815 (mpp) REVERT: B 287 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.6981 (mm-30) REVERT: B 313 GLN cc_start: 0.6621 (mp10) cc_final: 0.6283 (mp10) REVERT: B 415 MET cc_start: 0.8137 (tpp) cc_final: 0.7687 (mtt) REVERT: B 429 MET cc_start: 0.8576 (tmm) cc_final: 0.8174 (tmt) REVERT: B 486 ARG cc_start: 0.7005 (mtt90) cc_final: 0.6765 (mtt90) REVERT: B 540 ARG cc_start: 0.7402 (ttp80) cc_final: 0.6927 (ttp80) REVERT: B 565 GLU cc_start: 0.7415 (mt-10) cc_final: 0.7063 (mt-10) REVERT: B 594 LEU cc_start: 0.8340 (mt) cc_final: 0.8101 (mt) REVERT: B 595 THR cc_start: 0.8165 (OUTLIER) cc_final: 0.7934 (p) outliers start: 46 outliers final: 17 residues processed: 219 average time/residue: 0.5536 time to fit residues: 137.1283 Evaluate side-chains 200 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 173 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 297 CYS Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain D residue 109 LEU Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 595 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 23 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 188 optimal weight: 0.6980 chunk 60 optimal weight: 0.0970 chunk 169 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 383 GLN A 420 GLN C 233 GLN C 420 GLN D 383 GLN D 420 GLN B 420 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.217133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.146875 restraints weight = 17573.738| |-----------------------------------------------------------------------------| r_work (start): 0.3939 rms_B_bonded: 2.34 r_work: 0.3844 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3726 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17360 Z= 0.140 Angle : 0.558 9.904 23532 Z= 0.286 Chirality : 0.040 0.167 2652 Planarity : 0.003 0.037 2948 Dihedral : 4.820 27.551 2308 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.70 % Allowed : 16.90 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.19), residues: 2076 helix: 0.28 (0.16), residues: 1276 sheet: 0.38 (0.51), residues: 88 loop : -1.82 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 527 TYR 0.012 0.002 TYR B 270 PHE 0.024 0.001 PHE B 103 TRP 0.006 0.001 TRP C 574 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00330 (17348) covalent geometry : angle 0.55808 (23508) SS BOND : bond 0.00141 ( 12) SS BOND : angle 0.86507 ( 24) hydrogen bonds : bond 0.03085 ( 820) hydrogen bonds : angle 4.26601 ( 2328) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 175 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.5449 (mpp) cc_final: 0.4866 (mpp) REVERT: A 214 SER cc_start: 0.4108 (OUTLIER) cc_final: 0.3878 (t) REVERT: A 287 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7116 (mm-30) REVERT: A 314 ASN cc_start: 0.7798 (m-40) cc_final: 0.7596 (m-40) REVERT: A 415 MET cc_start: 0.8236 (mtp) cc_final: 0.7741 (mtt) REVERT: A 429 MET cc_start: 0.8628 (tmm) cc_final: 0.8216 (tmt) REVERT: A 486 ARG cc_start: 0.7261 (mtt90) cc_final: 0.6944 (mtt90) REVERT: A 565 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6877 (mt-10) REVERT: A 567 CYS cc_start: 0.6801 (OUTLIER) cc_final: 0.5989 (t) REVERT: A 595 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.7921 (p) REVERT: C 155 MET cc_start: 0.5275 (mpp) cc_final: 0.4695 (mpp) REVERT: C 232 VAL cc_start: 0.6374 (m) cc_final: 0.6135 (p) REVERT: C 287 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7684 (mm-30) REVERT: C 295 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6919 (pt0) REVERT: C 313 GLN cc_start: 0.6738 (mp10) cc_final: 0.6374 (mp10) REVERT: C 330 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7367 (tppt) REVERT: C 392 MET cc_start: 0.7931 (tpt) cc_final: 0.7314 (ttt) REVERT: C 415 MET cc_start: 0.8264 (mtp) cc_final: 0.7780 (mtt) REVERT: C 429 MET cc_start: 0.8596 (tmm) cc_final: 0.8197 (tmt) REVERT: C 486 ARG cc_start: 0.7345 (ttm170) cc_final: 0.6765 (ttm110) REVERT: C 565 GLU cc_start: 0.7356 (mt-10) cc_final: 0.7145 (mt-10) REVERT: C 595 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.7964 (p) REVERT: D 155 MET cc_start: 0.5433 (mpp) cc_final: 0.4831 (mpp) REVERT: D 287 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7130 (mm-30) REVERT: D 313 GLN cc_start: 0.6680 (mp10) cc_final: 0.6344 (mp10) REVERT: D 415 MET cc_start: 0.8169 (tpp) cc_final: 0.7705 (mtt) REVERT: D 429 MET cc_start: 0.8612 (tmm) cc_final: 0.8203 (tmt) REVERT: D 486 ARG cc_start: 0.7472 (mtt90) cc_final: 0.7087 (mtt90) REVERT: D 527 ARG cc_start: 0.6759 (OUTLIER) cc_final: 0.6418 (ptp-110) REVERT: D 540 ARG cc_start: 0.7475 (ttp-170) cc_final: 0.7113 (ttp80) REVERT: D 562 LYS cc_start: 0.7079 (OUTLIER) cc_final: 0.5845 (pttm) REVERT: D 565 GLU cc_start: 0.7396 (mt-10) cc_final: 0.7061 (mt-10) REVERT: D 567 CYS cc_start: 0.6537 (t) cc_final: 0.5313 (m) REVERT: D 595 THR cc_start: 0.8169 (OUTLIER) cc_final: 0.7889 (p) REVERT: B 155 MET cc_start: 0.5339 (mpp) cc_final: 0.4708 (mpp) REVERT: B 287 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: B 313 GLN cc_start: 0.6719 (mp10) cc_final: 0.6396 (mp10) REVERT: B 429 MET cc_start: 0.8619 (tmm) cc_final: 0.8206 (tmt) REVERT: B 486 ARG cc_start: 0.7254 (mtt90) cc_final: 0.6904 (mtt90) REVERT: B 562 LYS cc_start: 0.7046 (OUTLIER) cc_final: 0.6543 (mptt) REVERT: B 565 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6874 (mt-10) REVERT: B 595 THR cc_start: 0.8176 (OUTLIER) cc_final: 0.7896 (p) outliers start: 50 outliers final: 23 residues processed: 209 average time/residue: 0.5797 time to fit residues: 136.1279 Evaluate side-chains 209 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 295 GLU Chi-restraints excluded: chain C residue 297 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 527 ARG Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 562 LYS Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 595 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 164 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 0.0770 chunk 204 optimal weight: 3.9990 chunk 194 optimal weight: 0.8980 chunk 195 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 121 optimal weight: 0.4980 chunk 163 optimal weight: 4.9990 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 GLN D 420 GLN B 420 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.217546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.147046 restraints weight = 17744.759| |-----------------------------------------------------------------------------| r_work (start): 0.3946 rms_B_bonded: 2.37 r_work: 0.3850 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3732 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17360 Z= 0.131 Angle : 0.549 8.958 23532 Z= 0.283 Chirality : 0.040 0.164 2652 Planarity : 0.003 0.038 2948 Dihedral : 4.765 27.510 2308 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.38 % Allowed : 17.82 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.19), residues: 2076 helix: 0.33 (0.16), residues: 1272 sheet: 0.49 (0.52), residues: 88 loop : -1.70 (0.20), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 134 TYR 0.010 0.001 TYR C 456 PHE 0.027 0.001 PHE D 103 TRP 0.006 0.001 TRP A 574 HIS 0.004 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00308 (17348) covalent geometry : angle 0.54875 (23508) SS BOND : bond 0.00147 ( 12) SS BOND : angle 0.80756 ( 24) hydrogen bonds : bond 0.02996 ( 820) hydrogen bonds : angle 4.22164 ( 2328) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 178 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.5340 (mpp) cc_final: 0.4713 (mpp) REVERT: A 287 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7120 (mm-30) REVERT: A 314 ASN cc_start: 0.7811 (m-40) cc_final: 0.7609 (m-40) REVERT: A 415 MET cc_start: 0.8235 (mtp) cc_final: 0.7717 (mtt) REVERT: A 429 MET cc_start: 0.8653 (tmm) cc_final: 0.8238 (tmt) REVERT: A 486 ARG cc_start: 0.7279 (mtt90) cc_final: 0.6989 (mtt90) REVERT: A 540 ARG cc_start: 0.7545 (ttp80) cc_final: 0.6918 (ttp80) REVERT: A 565 GLU cc_start: 0.7349 (mt-10) cc_final: 0.6870 (mt-10) REVERT: A 594 LEU cc_start: 0.8438 (mt) cc_final: 0.8231 (mt) REVERT: A 595 THR cc_start: 0.8264 (OUTLIER) cc_final: 0.7958 (p) REVERT: C 155 MET cc_start: 0.5318 (mpp) cc_final: 0.4735 (mpp) REVERT: C 232 VAL cc_start: 0.6335 (m) cc_final: 0.6107 (p) REVERT: C 287 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7658 (mm-30) REVERT: C 313 GLN cc_start: 0.6718 (mp10) cc_final: 0.6367 (mp10) REVERT: C 315 MET cc_start: 0.7388 (mtp) cc_final: 0.7069 (mtt) REVERT: C 330 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7356 (tppt) REVERT: C 392 MET cc_start: 0.7980 (tpt) cc_final: 0.7348 (ttt) REVERT: C 415 MET cc_start: 0.8270 (mtp) cc_final: 0.7770 (mtt) REVERT: C 429 MET cc_start: 0.8627 (tmm) cc_final: 0.8224 (tmt) REVERT: C 486 ARG cc_start: 0.7347 (ttm170) cc_final: 0.6750 (ttm110) REVERT: C 565 GLU cc_start: 0.7359 (mt-10) cc_final: 0.6855 (mt-10) REVERT: C 567 CYS cc_start: 0.6722 (OUTLIER) cc_final: 0.5933 (t) REVERT: C 595 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.7998 (p) REVERT: D 155 MET cc_start: 0.5338 (OUTLIER) cc_final: 0.4716 (mpp) REVERT: D 287 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7144 (mm-30) REVERT: D 313 GLN cc_start: 0.6642 (mp10) cc_final: 0.6325 (mp10) REVERT: D 415 MET cc_start: 0.8191 (tpp) cc_final: 0.7798 (mtt) REVERT: D 429 MET cc_start: 0.8661 (tmm) cc_final: 0.8249 (tmt) REVERT: D 486 ARG cc_start: 0.7504 (mtt90) cc_final: 0.7109 (mtt90) REVERT: D 540 ARG cc_start: 0.7464 (ttp-170) cc_final: 0.7091 (ttp80) REVERT: D 562 LYS cc_start: 0.7066 (OUTLIER) cc_final: 0.6509 (mptt) REVERT: D 565 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6888 (mt-10) REVERT: D 567 CYS cc_start: 0.6536 (t) cc_final: 0.5209 (m) REVERT: D 594 LEU cc_start: 0.8428 (mt) cc_final: 0.8220 (mt) REVERT: D 595 THR cc_start: 0.8269 (OUTLIER) cc_final: 0.7971 (p) REVERT: B 155 MET cc_start: 0.5327 (mpp) cc_final: 0.4694 (mpp) REVERT: B 287 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7129 (mm-30) REVERT: B 313 GLN cc_start: 0.6667 (mp10) cc_final: 0.6347 (mp10) REVERT: B 415 MET cc_start: 0.8186 (mtp) cc_final: 0.7709 (mtt) REVERT: B 429 MET cc_start: 0.8618 (tmm) cc_final: 0.8207 (tmt) REVERT: B 486 ARG cc_start: 0.7254 (mtt90) cc_final: 0.6991 (mtt90) REVERT: B 562 LYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6506 (mptt) REVERT: B 565 GLU cc_start: 0.7318 (mt-10) cc_final: 0.6813 (mt-10) REVERT: B 594 LEU cc_start: 0.8450 (mt) cc_final: 0.8219 (mt) REVERT: B 595 THR cc_start: 0.8273 (OUTLIER) cc_final: 0.7962 (p) outliers start: 44 outliers final: 24 residues processed: 210 average time/residue: 0.5899 time to fit residues: 138.8791 Evaluate side-chains 207 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 297 CYS Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 562 LYS Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 595 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 134 optimal weight: 0.2980 chunk 6 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 172 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 187 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 5 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 GLN D 420 GLN B 420 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.216885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.146200 restraints weight = 17703.196| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.36 r_work: 0.3843 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17360 Z= 0.144 Angle : 0.562 8.403 23532 Z= 0.290 Chirality : 0.040 0.168 2652 Planarity : 0.004 0.068 2948 Dihedral : 4.791 27.691 2308 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.48 % Allowed : 17.87 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.18), residues: 2076 helix: 0.29 (0.16), residues: 1276 sheet: 0.62 (0.52), residues: 88 loop : -1.76 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 527 TYR 0.014 0.002 TYR C 266 PHE 0.029 0.001 PHE A 103 TRP 0.006 0.001 TRP A 574 HIS 0.004 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00340 (17348) covalent geometry : angle 0.56127 (23508) SS BOND : bond 0.00155 ( 12) SS BOND : angle 0.87797 ( 24) hydrogen bonds : bond 0.03117 ( 820) hydrogen bonds : angle 4.27073 ( 2328) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 170 time to evaluate : 0.597 Fit side-chains REVERT: A 155 MET cc_start: 0.5339 (mpp) cc_final: 0.4674 (mpp) REVERT: A 214 SER cc_start: 0.4168 (OUTLIER) cc_final: 0.3932 (t) REVERT: A 287 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7175 (mm-30) REVERT: A 429 MET cc_start: 0.8650 (tmm) cc_final: 0.8235 (tmt) REVERT: A 486 ARG cc_start: 0.7280 (mtt90) cc_final: 0.7006 (mtt90) REVERT: A 565 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6905 (mt-10) REVERT: A 595 THR cc_start: 0.8207 (OUTLIER) cc_final: 0.7887 (p) REVERT: C 155 MET cc_start: 0.5289 (mpp) cc_final: 0.4696 (mpp) REVERT: C 287 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7644 (mm-30) REVERT: C 313 GLN cc_start: 0.6721 (mp10) cc_final: 0.6380 (mp10) REVERT: C 330 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7376 (tppt) REVERT: C 392 MET cc_start: 0.7953 (tpt) cc_final: 0.7332 (ttt) REVERT: C 415 MET cc_start: 0.8229 (mtp) cc_final: 0.7670 (mtt) REVERT: C 429 MET cc_start: 0.8604 (tmm) cc_final: 0.8207 (tmt) REVERT: C 486 ARG cc_start: 0.7429 (ttm170) cc_final: 0.6874 (ttm110) REVERT: C 565 GLU cc_start: 0.7308 (mt-10) cc_final: 0.6862 (mt-10) REVERT: C 595 THR cc_start: 0.8251 (OUTLIER) cc_final: 0.7942 (p) REVERT: D 155 MET cc_start: 0.5450 (OUTLIER) cc_final: 0.4928 (mpp) REVERT: D 287 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7208 (mm-30) REVERT: D 313 GLN cc_start: 0.6664 (mp10) cc_final: 0.6349 (mp10) REVERT: D 429 MET cc_start: 0.8643 (tmm) cc_final: 0.8231 (tmt) REVERT: D 486 ARG cc_start: 0.7562 (mtt90) cc_final: 0.7148 (mtt90) REVERT: D 540 ARG cc_start: 0.7605 (ttp-170) cc_final: 0.7226 (ttp80) REVERT: D 562 LYS cc_start: 0.7069 (OUTLIER) cc_final: 0.5792 (pttm) REVERT: D 565 GLU cc_start: 0.7334 (mt-10) cc_final: 0.6990 (mt-10) REVERT: D 566 PHE cc_start: 0.7894 (p90) cc_final: 0.7615 (p90) REVERT: D 567 CYS cc_start: 0.6511 (t) cc_final: 0.5235 (m) REVERT: D 594 LEU cc_start: 0.8419 (mt) cc_final: 0.8191 (mt) REVERT: D 595 THR cc_start: 0.8224 (OUTLIER) cc_final: 0.7935 (p) REVERT: B 155 MET cc_start: 0.5518 (mpp) cc_final: 0.5005 (mpp) REVERT: B 287 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7190 (mm-30) REVERT: B 313 GLN cc_start: 0.6681 (mp10) cc_final: 0.6366 (mp10) REVERT: B 415 MET cc_start: 0.8299 (mtp) cc_final: 0.7814 (mtt) REVERT: B 429 MET cc_start: 0.8610 (tmm) cc_final: 0.8197 (tmt) REVERT: B 486 ARG cc_start: 0.7310 (mtt90) cc_final: 0.7046 (mtt90) REVERT: B 562 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.6560 (mptt) REVERT: B 565 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6941 (mt-10) REVERT: B 594 LEU cc_start: 0.8402 (mt) cc_final: 0.8199 (mt) REVERT: B 595 THR cc_start: 0.8220 (OUTLIER) cc_final: 0.7913 (p) outliers start: 46 outliers final: 27 residues processed: 205 average time/residue: 0.5479 time to fit residues: 126.3045 Evaluate side-chains 207 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 167 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 508 ASP Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 562 LYS Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 595 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 32 optimal weight: 0.5980 chunk 157 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 160 optimal weight: 0.9990 chunk 98 optimal weight: 0.4980 chunk 202 optimal weight: 7.9990 chunk 185 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 GLN D 420 GLN B 420 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4480 r_free = 0.4480 target = 0.217947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.148175 restraints weight = 17549.865| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 2.37 r_work: 0.3855 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3730 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17360 Z= 0.123 Angle : 0.545 7.956 23532 Z= 0.280 Chirality : 0.039 0.165 2652 Planarity : 0.003 0.066 2948 Dihedral : 4.704 27.711 2308 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.27 % Allowed : 18.03 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.46 (0.19), residues: 2076 helix: 0.37 (0.16), residues: 1276 sheet: 0.84 (0.52), residues: 88 loop : -1.63 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 527 TYR 0.010 0.001 TYR A 309 PHE 0.031 0.001 PHE C 103 TRP 0.005 0.001 TRP B 281 HIS 0.004 0.001 HIS C 275 Details of bonding type rmsd covalent geometry : bond 0.00288 (17348) covalent geometry : angle 0.54464 (23508) SS BOND : bond 0.00140 ( 12) SS BOND : angle 0.76618 ( 24) hydrogen bonds : bond 0.02941 ( 820) hydrogen bonds : angle 4.16272 ( 2328) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4152 Ramachandran restraints generated. 2076 Oldfield, 0 Emsley, 2076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 0.603 Fit side-chains REVERT: A 155 MET cc_start: 0.5414 (mpp) cc_final: 0.4787 (mpp) REVERT: A 214 SER cc_start: 0.4208 (OUTLIER) cc_final: 0.3979 (t) REVERT: A 287 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7047 (mm-30) REVERT: A 415 MET cc_start: 0.8129 (mtp) cc_final: 0.7644 (mtt) REVERT: A 429 MET cc_start: 0.8607 (tmm) cc_final: 0.8190 (tmt) REVERT: A 486 ARG cc_start: 0.7230 (mtt90) cc_final: 0.6947 (mtt90) REVERT: A 565 GLU cc_start: 0.7411 (mt-10) cc_final: 0.6991 (mt-10) REVERT: A 567 CYS cc_start: 0.6662 (OUTLIER) cc_final: 0.5890 (t) REVERT: A 595 THR cc_start: 0.8301 (OUTLIER) cc_final: 0.8008 (p) REVERT: C 155 MET cc_start: 0.5173 (mpp) cc_final: 0.4605 (mpp) REVERT: C 287 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7535 (mm-30) REVERT: C 313 GLN cc_start: 0.6627 (mp10) cc_final: 0.6306 (mp10) REVERT: C 330 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7327 (tppt) REVERT: C 392 MET cc_start: 0.7923 (tpt) cc_final: 0.7290 (ttt) REVERT: C 415 MET cc_start: 0.8130 (mtp) cc_final: 0.7544 (mtt) REVERT: C 429 MET cc_start: 0.8579 (tmm) cc_final: 0.8178 (tmt) REVERT: C 486 ARG cc_start: 0.7297 (ttm170) cc_final: 0.7075 (mtt90) REVERT: C 565 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6945 (mt-10) REVERT: C 567 CYS cc_start: 0.6630 (OUTLIER) cc_final: 0.5865 (t) REVERT: C 595 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.7940 (p) REVERT: D 155 MET cc_start: 0.5436 (OUTLIER) cc_final: 0.4868 (mpp) REVERT: D 287 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7094 (mm-30) REVERT: D 313 GLN cc_start: 0.6632 (mp10) cc_final: 0.6321 (mp10) REVERT: D 415 MET cc_start: 0.8281 (mtp) cc_final: 0.7765 (mtt) REVERT: D 429 MET cc_start: 0.8602 (tmm) cc_final: 0.8196 (tmt) REVERT: D 486 ARG cc_start: 0.7447 (mtt90) cc_final: 0.7042 (mtt90) REVERT: D 540 ARG cc_start: 0.7410 (ttp-170) cc_final: 0.6921 (ttp80) REVERT: D 562 LYS cc_start: 0.7050 (OUTLIER) cc_final: 0.6455 (mptt) REVERT: D 565 GLU cc_start: 0.7381 (mt-10) cc_final: 0.6897 (mt-10) REVERT: D 566 PHE cc_start: 0.7817 (p90) cc_final: 0.7547 (p90) REVERT: D 567 CYS cc_start: 0.6510 (t) cc_final: 0.5237 (m) REVERT: D 594 LEU cc_start: 0.8407 (mt) cc_final: 0.8170 (mt) REVERT: D 595 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.7974 (p) REVERT: B 155 MET cc_start: 0.5579 (mpp) cc_final: 0.5012 (mpp) REVERT: B 287 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7042 (mm-30) REVERT: B 313 GLN cc_start: 0.6640 (mp10) cc_final: 0.6325 (mp10) REVERT: B 415 MET cc_start: 0.8180 (mtp) cc_final: 0.7723 (mtt) REVERT: B 429 MET cc_start: 0.8576 (tmm) cc_final: 0.8171 (tmt) REVERT: B 486 ARG cc_start: 0.7134 (mtt90) cc_final: 0.6901 (mtt90) REVERT: B 562 LYS cc_start: 0.6987 (OUTLIER) cc_final: 0.6468 (mptt) REVERT: B 565 GLU cc_start: 0.7396 (mt-10) cc_final: 0.6962 (mt-10) REVERT: B 567 CYS cc_start: 0.6506 (t) cc_final: 0.5203 (m) REVERT: B 594 LEU cc_start: 0.8387 (mt) cc_final: 0.8142 (mt) REVERT: B 595 THR cc_start: 0.8208 (OUTLIER) cc_final: 0.7924 (p) outliers start: 42 outliers final: 25 residues processed: 200 average time/residue: 0.5833 time to fit residues: 131.3912 Evaluate side-chains 209 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 234 TYR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 287 GLU Chi-restraints excluded: chain A residue 295 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 270 TYR Chi-restraints excluded: chain C residue 287 GLU Chi-restraints excluded: chain C residue 320 VAL Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 560 LEU Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain D residue 155 MET Chi-restraints excluded: chain D residue 234 TYR Chi-restraints excluded: chain D residue 270 TYR Chi-restraints excluded: chain D residue 287 GLU Chi-restraints excluded: chain D residue 295 GLU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 562 LYS Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain B residue 234 TYR Chi-restraints excluded: chain B residue 270 TYR Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 295 GLU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 508 ASP Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 562 LYS Chi-restraints excluded: chain B residue 595 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 52 optimal weight: 10.0000 chunk 113 optimal weight: 3.9990 chunk 136 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 110 optimal weight: 7.9990 chunk 144 optimal weight: 4.9990 chunk 181 optimal weight: 0.0040 chunk 3 optimal weight: 0.9980 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 GLN D 420 GLN B 420 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.215687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.145271 restraints weight = 17598.284| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 2.34 r_work: 0.3813 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3688 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17360 Z= 0.186 Angle : 0.598 7.799 23532 Z= 0.308 Chirality : 0.042 0.173 2652 Planarity : 0.004 0.066 2948 Dihedral : 4.920 27.596 2308 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.32 % Allowed : 18.25 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.18), residues: 2076 helix: 0.23 (0.15), residues: 1276 sheet: 1.04 (0.60), residues: 48 loop : -1.74 (0.19), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 527 TYR 0.014 0.002 TYR D 524 PHE 0.033 0.002 PHE C 103 TRP 0.007 0.001 TRP B 372 HIS 0.004 0.001 HIS D 275 Details of bonding type rmsd covalent geometry : bond 0.00443 (17348) covalent geometry : angle 0.59733 (23508) SS BOND : bond 0.00208 ( 12) SS BOND : angle 1.02513 ( 24) hydrogen bonds : bond 0.03423 ( 820) hydrogen bonds : angle 4.41089 ( 2328) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7691.97 seconds wall clock time: 131 minutes 13.77 seconds (7873.77 seconds total)