Starting phenix.real_space_refine on Sun Jun 15 04:55:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j36_61107/06_2025/9j36_61107.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j36_61107/06_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_61107/06_2025/9j36_61107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j36_61107/06_2025/9j36_61107.map" model { file = "/net/cci-nas-00/data/ceres_data/9j36_61107/06_2025/9j36_61107.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j36_61107/06_2025/9j36_61107.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.099 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.30, per 1000 atoms: 0.67 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: 4.23 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.95 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: 5.77 Time building geometry restraints manager: 5.13 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 41.050 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:16.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.730 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.013 0.002 TRP B 372 HIS 0.006 0.002 HIS C 154 PHE 0.020 0.003 PHE C 363 TYR 0.021 0.004 TYR C 270 ARG 0.007 0.001 ARG B 433 Details of bonding type rmsd hydrogen bonds : bond 0.22079 ( 820) hydrogen bonds : angle 8.65320 ( 2328) SS BOND : bond 0.00633 ( 12) SS BOND : angle 2.48401 ( 24) covalent geometry : bond 0.01018 (17348) covalent geometry : angle 1.29335 (23508) *********************** 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 : 2.196 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: 1.4799 time to fit residues: 415.9787 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 : 1.998 ------------------------------------------------------------------------------- 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 175 optimal weight: 0.5980 chunk 157 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 163 optimal weight: 9.9990 chunk 63 optimal weight: 0.0980 chunk 99 optimal weight: 0.9990 chunk 121 optimal weight: 0.8980 chunk 188 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 HIS A 289 ASN A 340 ASN ** A 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN C 154 HIS C 289 ASN C 340 ASN ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 HIS D 289 ASN D 340 ASN ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN B 154 HIS B 289 ASN B 340 ASN ** B 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 414 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.219273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.151750 restraints weight = 17711.268| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 2.33 r_work: 0.3866 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3746 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17360 Z= 0.121 Angle : 0.591 8.261 23532 Z= 0.314 Chirality : 0.040 0.147 2652 Planarity : 0.004 0.039 2948 Dihedral : 5.862 32.925 2320 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.59 % Allowed : 13.07 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.17), residues: 2076 helix: -1.26 (0.14), residues: 1276 sheet: -1.90 (0.41), residues: 128 loop : -1.69 (0.20), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 574 HIS 0.003 0.001 HIS D 275 PHE 0.012 0.001 PHE D 210 TYR 0.012 0.002 TYR D 270 ARG 0.002 0.000 ARG D 589 Details of bonding type rmsd hydrogen bonds : bond 0.03505 ( 820) hydrogen bonds : angle 4.85405 ( 2328) SS BOND : bond 0.00125 ( 12) SS BOND : angle 0.78711 ( 24) covalent geometry : bond 0.00269 (17348) covalent geometry : angle 0.59068 (23508) *********************** 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 249 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 201 time to evaluate : 1.752 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.5999 (mpp) cc_final: 0.5205 (mpp) REVERT: A 392 MET cc_start: 0.8268 (ttt) cc_final: 0.7708 (tmt) REVERT: A 429 MET cc_start: 0.8626 (tmm) cc_final: 0.8234 (tmt) REVERT: A 486 ARG cc_start: 0.7445 (mtt90) cc_final: 0.6916 (mtt90) REVERT: A 535 MET cc_start: 0.7996 (ttm) cc_final: 0.7787 (ttp) REVERT: A 540 ARG cc_start: 0.7440 (ttp-170) cc_final: 0.7117 (ttp80) REVERT: A 565 GLU cc_start: 0.7225 (mt-10) cc_final: 0.6886 (mt-10) REVERT: A 594 LEU cc_start: 0.8406 (mt) cc_final: 0.8196 (mt) REVERT: C 155 MET cc_start: 0.5429 (mpp) cc_final: 0.5031 (mpp) REVERT: C 214 SER cc_start: 0.4196 (OUTLIER) cc_final: 0.3748 (t) REVERT: C 287 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7285 (tm-30) REVERT: C 289 ASN cc_start: 0.7986 (t160) cc_final: 0.7781 (t0) REVERT: C 313 GLN cc_start: 0.6303 (mp10) cc_final: 0.5929 (mp10) REVERT: C 330 LYS cc_start: 0.8084 (OUTLIER) cc_final: 0.7026 (tppt) REVERT: C 336 ASP cc_start: 0.8128 (m-30) cc_final: 0.7880 (m-30) REVERT: C 415 MET cc_start: 0.8156 (tpp) cc_final: 0.7746 (mtt) REVERT: C 429 MET cc_start: 0.8588 (tmm) cc_final: 0.8269 (tmt) REVERT: C 486 ARG cc_start: 0.7359 (mtt90) cc_final: 0.6898 (mtt90) REVERT: C 562 LYS cc_start: 0.7260 (mptt) cc_final: 0.5992 (pttm) REVERT: C 565 GLU cc_start: 0.7323 (mt-10) cc_final: 0.6973 (mt-10) REVERT: D 155 MET cc_start: 0.5926 (mpp) cc_final: 0.5102 (mpp) REVERT: D 392 MET cc_start: 0.8211 (ttt) cc_final: 0.7674 (tmt) REVERT: D 415 MET cc_start: 0.8271 (tpp) cc_final: 0.7894 (mtt) REVERT: D 429 MET cc_start: 0.8638 (tmm) cc_final: 0.8249 (tmt) REVERT: D 486 ARG cc_start: 0.7410 (mtt90) cc_final: 0.6873 (mtt90) REVERT: D 540 ARG cc_start: 0.7449 (ttp-170) cc_final: 0.7215 (ttp80) REVERT: D 562 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.5808 (pttm) REVERT: D 565 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6991 (mt-10) REVERT: B 155 MET cc_start: 0.5852 (mpp) cc_final: 0.5110 (mpp) REVERT: B 415 MET cc_start: 0.8227 (tpp) cc_final: 0.7828 (mtt) REVERT: B 429 MET cc_start: 0.8619 (tmm) cc_final: 0.8258 (tmt) REVERT: B 486 ARG cc_start: 0.7458 (mtt90) cc_final: 0.6927 (mtt90) REVERT: B 535 MET cc_start: 0.7972 (ttm) cc_final: 0.7725 (ttp) REVERT: B 540 ARG cc_start: 0.7382 (ttp-170) cc_final: 0.7143 (ttp80) REVERT: B 562 LYS cc_start: 0.6989 (OUTLIER) cc_final: 0.5718 (pttm) REVERT: B 565 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6927 (mt-10) outliers start: 48 outliers final: 19 residues processed: 231 average time/residue: 1.0999 time to fit residues: 287.4782 Evaluate side-chains 181 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 1.623 ------------------------------------------------------------------------------- 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 103 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 107 optimal weight: 0.0970 chunk 203 optimal weight: 5.9990 chunk 114 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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** A 420 GLN ** C 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 420 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.216863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.147672 restraints weight = 17595.933| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.35 r_work: 0.3832 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3707 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7053 moved from start: 0.2280 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= 0.145 Angle : 0.584 8.011 23532 Z= 0.305 Chirality : 0.040 0.158 2652 Planarity : 0.004 0.053 2948 Dihedral : 5.393 31.579 2308 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.32 % Allowed : 15.39 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.18), residues: 2076 helix: -0.51 (0.15), residues: 1268 sheet: -0.87 (0.45), residues: 88 loop : -1.88 (0.20), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 574 HIS 0.004 0.001 HIS C 275 PHE 0.013 0.001 PHE B 363 TYR 0.012 0.002 TYR A 266 ARG 0.002 0.000 ARG A 486 Details of bonding type rmsd hydrogen bonds : bond 0.03367 ( 820) hydrogen bonds : angle 4.59291 ( 2328) SS BOND : bond 0.00148 ( 12) SS BOND : angle 0.82355 ( 24) covalent geometry : bond 0.00336 (17348) covalent geometry : angle 0.58365 (23508) *********************** 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 213 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 170 time to evaluate : 1.776 Fit side-chains REVERT: A 155 MET cc_start: 0.5804 (mpp) cc_final: 0.5064 (mpp) REVERT: A 287 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7136 (mm-30) REVERT: A 415 MET cc_start: 0.8142 (mtp) cc_final: 0.7552 (mtt) REVERT: A 419 LEU cc_start: 0.8311 (OUTLIER) cc_final: 0.8085 (mp) REVERT: A 429 MET cc_start: 0.8531 (tmm) cc_final: 0.8189 (tmt) REVERT: A 486 ARG cc_start: 0.7107 (mtt90) cc_final: 0.6745 (mtt90) REVERT: A 540 ARG cc_start: 0.7433 (ttp-170) cc_final: 0.7061 (ttp80) REVERT: A 565 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6905 (mt-10) REVERT: C 155 MET cc_start: 0.5364 (mpp) cc_final: 0.4925 (mpp) REVERT: C 287 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7002 (tm-30) REVERT: C 313 GLN cc_start: 0.6537 (mp10) cc_final: 0.6050 (mp10) REVERT: C 330 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7007 (tppt) REVERT: C 336 ASP cc_start: 0.8146 (m-30) cc_final: 0.7810 (m-30) REVERT: C 392 MET cc_start: 0.7883 (tpt) cc_final: 0.7242 (ttt) REVERT: C 415 MET cc_start: 0.8164 (tpp) cc_final: 0.7638 (mtt) REVERT: C 429 MET cc_start: 0.8539 (tmm) cc_final: 0.8214 (tmt) REVERT: C 486 ARG cc_start: 0.7239 (mtt90) cc_final: 0.6818 (mtt90) REVERT: C 565 GLU cc_start: 0.7379 (mt-10) cc_final: 0.6988 (mt-10) REVERT: D 155 MET cc_start: 0.5725 (mpp) cc_final: 0.5136 (mpp) REVERT: D 287 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7106 (mm-30) REVERT: D 314 ASN cc_start: 0.7562 (m110) cc_final: 0.7346 (m-40) REVERT: D 315 MET cc_start: 0.7346 (mtp) cc_final: 0.7116 (mtt) REVERT: D 415 MET cc_start: 0.8113 (tpp) cc_final: 0.7899 (mtp) REVERT: D 429 MET cc_start: 0.8539 (tmm) cc_final: 0.8203 (tmt) REVERT: D 486 ARG cc_start: 0.7258 (mtt90) cc_final: 0.6886 (mtt90) REVERT: D 540 ARG cc_start: 0.7438 (ttp-170) cc_final: 0.7053 (ttp80) REVERT: D 562 LYS cc_start: 0.7071 (OUTLIER) cc_final: 0.5782 (pttm) REVERT: D 565 GLU cc_start: 0.7340 (mt-10) cc_final: 0.7013 (mt-10) REVERT: B 155 MET cc_start: 0.5720 (mpp) cc_final: 0.5128 (mpp) REVERT: B 287 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7089 (mm-30) REVERT: B 314 ASN cc_start: 0.7588 (m110) cc_final: 0.7381 (m-40) REVERT: B 415 MET cc_start: 0.8160 (tpp) cc_final: 0.7891 (mtp) REVERT: B 419 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8091 (mp) REVERT: B 429 MET cc_start: 0.8556 (tmm) cc_final: 0.8216 (tmt) REVERT: B 486 ARG cc_start: 0.7260 (mtt90) cc_final: 0.6944 (mtt90) REVERT: B 540 ARG cc_start: 0.7474 (ttp-170) cc_final: 0.7052 (ttp80) REVERT: B 562 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.5846 (pttm) REVERT: B 565 GLU cc_start: 0.7300 (mt-10) cc_final: 0.7053 (mt-10) outliers start: 43 outliers final: 18 residues processed: 196 average time/residue: 1.3777 time to fit residues: 304.5895 Evaluate side-chains 175 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 1.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 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 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 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 229 ILE Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 419 LEU 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 73 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 162 optimal weight: 7.9990 chunk 83 optimal weight: 0.5980 chunk 191 optimal weight: 1.9990 chunk 104 optimal weight: 20.0000 chunk 183 optimal weight: 0.0870 chunk 7 optimal weight: 9.9990 chunk 147 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 overall best weight: 0.8760 ------------------------------------------------------------------------------- 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** C 420 GLN ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.217707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.147776 restraints weight = 17363.949| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 2.30 r_work: 0.3832 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3714 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.2575 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= 0.134 Angle : 0.553 7.281 23532 Z= 0.290 Chirality : 0.040 0.156 2652 Planarity : 0.003 0.045 2948 Dihedral : 5.126 29.921 2308 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.65 % Allowed : 15.77 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.18), residues: 2076 helix: -0.18 (0.15), residues: 1280 sheet: -0.27 (0.48), residues: 88 loop : -2.02 (0.20), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 574 HIS 0.005 0.001 HIS C 275 PHE 0.021 0.001 PHE C 103 TYR 0.010 0.002 TYR D 367 ARG 0.003 0.000 ARG D 450 Details of bonding type rmsd hydrogen bonds : bond 0.03142 ( 820) hydrogen bonds : angle 4.41303 ( 2328) SS BOND : bond 0.00144 ( 12) SS BOND : angle 0.80187 ( 24) covalent geometry : bond 0.00314 (17348) covalent geometry : angle 0.55248 (23508) *********************** 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 220 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 171 time to evaluate : 1.769 Fit side-chains REVERT: A 155 MET cc_start: 0.5473 (mpp) cc_final: 0.4761 (mpp) REVERT: A 214 SER cc_start: 0.4241 (OUTLIER) cc_final: 0.3965 (t) REVERT: A 287 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7114 (mm-30) REVERT: A 315 MET cc_start: 0.7248 (mtp) cc_final: 0.7047 (mtt) REVERT: A 415 MET cc_start: 0.8213 (mtp) cc_final: 0.7645 (mtt) REVERT: A 419 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.8084 (mp) REVERT: A 429 MET cc_start: 0.8579 (tmm) cc_final: 0.8189 (tmt) REVERT: A 486 ARG cc_start: 0.7157 (mtt90) cc_final: 0.6768 (mtt90) REVERT: A 540 ARG cc_start: 0.7435 (ttp-170) cc_final: 0.6930 (ttp80) REVERT: A 565 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6838 (mt-10) REVERT: A 595 THR cc_start: 0.8167 (OUTLIER) cc_final: 0.7824 (p) REVERT: C 155 MET cc_start: 0.5205 (mpp) cc_final: 0.4691 (mpp) REVERT: C 232 VAL cc_start: 0.6253 (m) cc_final: 0.5896 (p) REVERT: C 287 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7057 (tm-30) REVERT: C 313 GLN cc_start: 0.6631 (mp10) cc_final: 0.6268 (mp10) REVERT: C 330 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7087 (tppt) REVERT: C 392 MET cc_start: 0.7978 (tpt) cc_final: 0.7331 (ttt) REVERT: C 429 MET cc_start: 0.8592 (tmm) cc_final: 0.8200 (tmt) REVERT: C 486 ARG cc_start: 0.7427 (mtt90) cc_final: 0.6903 (mtt90) REVERT: C 544 GLU cc_start: 0.7185 (OUTLIER) cc_final: 0.6189 (tp30) REVERT: C 565 GLU cc_start: 0.7351 (mt-10) cc_final: 0.6928 (mt-10) REVERT: C 595 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7767 (p) REVERT: D 155 MET cc_start: 0.5472 (mpp) cc_final: 0.4897 (mpp) REVERT: D 287 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7111 (mm-30) REVERT: D 415 MET cc_start: 0.8200 (tpp) cc_final: 0.7889 (tpp) REVERT: D 419 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8081 (mp) REVERT: D 429 MET cc_start: 0.8581 (tmm) cc_final: 0.8187 (tmt) REVERT: D 486 ARG cc_start: 0.7272 (mtt90) cc_final: 0.6889 (mtt90) REVERT: D 540 ARG cc_start: 0.7487 (ttp-170) cc_final: 0.6973 (ttp80) REVERT: D 544 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.6281 (tp30) REVERT: D 562 LYS cc_start: 0.7059 (OUTLIER) cc_final: 0.5778 (pttm) REVERT: D 565 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6924 (mt-10) REVERT: D 595 THR cc_start: 0.8119 (OUTLIER) cc_final: 0.7785 (p) REVERT: B 155 MET cc_start: 0.5529 (mpp) cc_final: 0.4931 (mpp) REVERT: B 287 GLU cc_start: 0.8019 (OUTLIER) cc_final: 0.7124 (mm-30) REVERT: B 415 MET cc_start: 0.8198 (tpp) cc_final: 0.7879 (tpp) REVERT: B 419 LEU cc_start: 0.8302 (OUTLIER) cc_final: 0.8101 (mp) REVERT: B 429 MET cc_start: 0.8580 (tmm) cc_final: 0.8169 (tmt) REVERT: B 486 ARG cc_start: 0.7282 (mtt90) cc_final: 0.6836 (mtt90) REVERT: B 540 ARG cc_start: 0.7465 (ttp-170) cc_final: 0.7071 (ttp80) REVERT: B 562 LYS cc_start: 0.7054 (OUTLIER) cc_final: 0.5764 (pttm) REVERT: B 565 GLU cc_start: 0.7331 (mt-10) cc_final: 0.6970 (mt-10) REVERT: B 595 THR cc_start: 0.8154 (OUTLIER) cc_final: 0.7817 (p) outliers start: 49 outliers final: 16 residues processed: 200 average time/residue: 1.2221 time to fit residues: 275.5337 Evaluate side-chains 195 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 1.773 ------------------------------------------------------------------------------- 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 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 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 287 GLU Chi-restraints excluded: chain D residue 320 VAL Chi-restraints excluded: chain D residue 419 LEU Chi-restraints excluded: chain D residue 462 LEU 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 214 SER Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 287 GLU Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 419 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 9 optimal weight: 20.0000 chunk 99 optimal weight: 10.0000 chunk 111 optimal weight: 20.0000 chunk 185 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 128 optimal weight: 4.9990 chunk 194 optimal weight: 0.0870 chunk 193 optimal weight: 0.7980 chunk 157 optimal weight: 0.9990 chunk 184 optimal weight: 0.6980 chunk 82 optimal weight: 0.9980 overall best weight: 0.7160 ------------------------------------------------------------------------------- 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 420 GLN D 124 ASN ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.218309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.148298 restraints weight = 17528.469| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.32 r_work: 0.3834 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3712 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.2747 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= 0.119 Angle : 0.528 7.151 23532 Z= 0.277 Chirality : 0.039 0.157 2652 Planarity : 0.003 0.041 2948 Dihedral : 4.935 27.799 2308 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.02 % Allowed : 15.71 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.18), residues: 2076 helix: 0.09 (0.16), residues: 1276 sheet: 0.10 (0.50), residues: 88 loop : -1.86 (0.20), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 574 HIS 0.005 0.001 HIS C 275 PHE 0.023 0.001 PHE B 103 TYR 0.011 0.001 TYR A 266 ARG 0.006 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.02940 ( 820) hydrogen bonds : angle 4.27802 ( 2328) SS BOND : bond 0.00111 ( 12) SS BOND : angle 0.75168 ( 24) covalent geometry : bond 0.00277 (17348) covalent geometry : angle 0.52780 (23508) *********************** 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 225 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 169 time to evaluate : 1.800 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.5518 (mpp) cc_final: 0.4847 (mpp) REVERT: A 214 SER cc_start: 0.4192 (OUTLIER) cc_final: 0.3948 (t) REVERT: A 287 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.6979 (mm-30) REVERT: A 419 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.8055 (mp) REVERT: A 429 MET cc_start: 0.8548 (tmm) cc_final: 0.8158 (tmt) REVERT: A 486 ARG cc_start: 0.7169 (mtt90) cc_final: 0.6793 (mtt90) REVERT: A 540 ARG cc_start: 0.7392 (ttp-170) cc_final: 0.6893 (ttp80) REVERT: A 565 GLU cc_start: 0.7395 (mt-10) cc_final: 0.6903 (mt-10) REVERT: A 595 THR cc_start: 0.8219 (OUTLIER) cc_final: 0.7892 (p) REVERT: C 155 MET cc_start: 0.5186 (mpp) cc_final: 0.4597 (mpp) REVERT: C 232 VAL cc_start: 0.6303 (m) cc_final: 0.5979 (p) REVERT: C 287 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7420 (mm-30) REVERT: C 313 GLN cc_start: 0.6711 (mp10) cc_final: 0.6300 (mp10) REVERT: C 330 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7082 (tppt) REVERT: C 392 MET cc_start: 0.7884 (tpt) cc_final: 0.7249 (ttt) REVERT: C 429 MET cc_start: 0.8535 (tmm) cc_final: 0.8145 (tmt) REVERT: C 565 GLU cc_start: 0.7393 (mt-10) cc_final: 0.6901 (mt-10) REVERT: C 595 THR cc_start: 0.8163 (OUTLIER) cc_final: 0.7830 (p) REVERT: D 155 MET cc_start: 0.5537 (mpp) cc_final: 0.4934 (mpp) REVERT: D 287 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7000 (mm-30) REVERT: D 419 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8074 (mp) REVERT: D 429 MET cc_start: 0.8539 (tmm) cc_final: 0.8150 (tmt) REVERT: D 486 ARG cc_start: 0.7177 (mtt90) cc_final: 0.6802 (mtt90) REVERT: D 530 ASP cc_start: 0.7247 (m-30) cc_final: 0.7021 (m-30) REVERT: D 540 ARG cc_start: 0.7438 (ttp-170) cc_final: 0.6924 (ttp80) REVERT: D 562 LYS cc_start: 0.7062 (OUTLIER) cc_final: 0.5800 (pttm) REVERT: D 565 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7059 (mt-10) REVERT: D 594 LEU cc_start: 0.8374 (mt) cc_final: 0.8155 (mt) REVERT: D 595 THR cc_start: 0.8150 (OUTLIER) cc_final: 0.7863 (p) REVERT: B 155 MET cc_start: 0.5485 (mpp) cc_final: 0.4920 (mpp) REVERT: B 287 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7042 (mm-30) REVERT: B 313 GLN cc_start: 0.6594 (mp10) cc_final: 0.6236 (mp10) REVERT: B 429 MET cc_start: 0.8557 (tmm) cc_final: 0.8153 (tmt) REVERT: B 486 ARG cc_start: 0.7142 (mtt90) cc_final: 0.6811 (mtt90) REVERT: B 540 ARG cc_start: 0.7458 (ttp-170) cc_final: 0.7070 (ttp80) REVERT: B 562 LYS cc_start: 0.7078 (OUTLIER) cc_final: 0.5808 (pttm) REVERT: B 565 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6983 (mt-10) REVERT: B 595 THR cc_start: 0.8205 (OUTLIER) cc_final: 0.7875 (p) outliers start: 56 outliers final: 27 residues processed: 206 average time/residue: 1.2634 time to fit residues: 291.7961 Evaluate side-chains 203 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 162 time to evaluate : 1.953 ------------------------------------------------------------------------------- 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 270 TYR Chi-restraints excluded: chain C residue 287 GLU 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 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 419 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 122 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 107 optimal weight: 0.0370 chunk 183 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 99 optimal weight: 0.4980 chunk 205 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 57 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 overall best weight: 0.9062 ------------------------------------------------------------------------------- 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 414 ASN C 420 GLN ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.216723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.146677 restraints weight = 17718.928| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 2.35 r_work: 0.3844 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3725 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.2867 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= 0.137 Angle : 0.544 6.931 23532 Z= 0.285 Chirality : 0.040 0.162 2652 Planarity : 0.003 0.039 2948 Dihedral : 4.918 27.981 2308 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.29 % Allowed : 16.14 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.18), residues: 2076 helix: 0.12 (0.16), residues: 1280 sheet: 0.16 (0.50), residues: 88 loop : -1.91 (0.20), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 574 HIS 0.004 0.001 HIS C 275 PHE 0.024 0.001 PHE B 103 TYR 0.010 0.002 TYR B 367 ARG 0.009 0.000 ARG D 527 Details of bonding type rmsd hydrogen bonds : bond 0.03083 ( 820) hydrogen bonds : angle 4.33094 ( 2328) SS BOND : bond 0.00146 ( 12) SS BOND : angle 0.85364 ( 24) covalent geometry : bond 0.00321 (17348) covalent geometry : angle 0.54323 (23508) *********************** 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 233 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 172 time to evaluate : 2.580 Fit side-chains REVERT: A 155 MET cc_start: 0.5563 (mpp) cc_final: 0.4914 (mpp) REVERT: A 214 SER cc_start: 0.4080 (OUTLIER) cc_final: 0.3853 (t) REVERT: A 287 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7185 (mm-30) REVERT: A 295 GLU cc_start: 0.7082 (OUTLIER) cc_final: 0.6867 (pt0) REVERT: A 415 MET cc_start: 0.8223 (mtp) cc_final: 0.7765 (mtt) REVERT: A 429 MET cc_start: 0.8634 (tmm) cc_final: 0.8224 (tmt) REVERT: A 486 ARG cc_start: 0.7246 (mtt90) cc_final: 0.6837 (mtt90) REVERT: A 540 ARG cc_start: 0.7479 (ttp-170) cc_final: 0.6992 (ttp80) REVERT: A 565 GLU cc_start: 0.7306 (mt-10) cc_final: 0.6854 (mt-10) REVERT: A 595 THR cc_start: 0.8290 (OUTLIER) cc_final: 0.7966 (p) REVERT: C 155 MET cc_start: 0.5278 (mpp) cc_final: 0.4691 (mpp) REVERT: C 232 VAL cc_start: 0.6300 (m) cc_final: 0.6022 (p) REVERT: C 287 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7629 (mm-30) REVERT: C 313 GLN cc_start: 0.6791 (mp10) cc_final: 0.6408 (mp10) REVERT: C 330 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7280 (tppt) REVERT: C 392 MET cc_start: 0.7942 (tpt) cc_final: 0.7327 (ttt) REVERT: C 414 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8239 (m110) REVERT: C 415 MET cc_start: 0.8329 (mtp) cc_final: 0.7739 (mtt) REVERT: C 429 MET cc_start: 0.8596 (tmm) cc_final: 0.8200 (tmt) REVERT: C 486 ARG cc_start: 0.7260 (ttm170) cc_final: 0.6709 (ttm110) REVERT: C 565 GLU cc_start: 0.7382 (mt-10) cc_final: 0.6902 (mt-10) REVERT: C 595 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7877 (p) REVERT: D 155 MET cc_start: 0.5554 (mpp) cc_final: 0.4844 (mpp) REVERT: D 287 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7193 (mm-30) REVERT: D 313 GLN cc_start: 0.6718 (mp10) cc_final: 0.6373 (mp10) REVERT: D 415 MET cc_start: 0.8233 (tpp) cc_final: 0.7867 (mtt) REVERT: D 429 MET cc_start: 0.8619 (tmm) cc_final: 0.8214 (tmt) REVERT: D 486 ARG cc_start: 0.7299 (mtt90) cc_final: 0.6936 (mtt90) REVERT: D 540 ARG cc_start: 0.7526 (ttp-170) cc_final: 0.7024 (ttp80) REVERT: D 562 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6665 (mptt) REVERT: D 565 GLU cc_start: 0.7358 (mt-10) cc_final: 0.6939 (mt-10) REVERT: D 594 LEU cc_start: 0.8455 (mt) cc_final: 0.8248 (mt) REVERT: D 595 THR cc_start: 0.8206 (OUTLIER) cc_final: 0.7906 (p) REVERT: B 155 MET cc_start: 0.5534 (mpp) cc_final: 0.4927 (mpp) REVERT: B 287 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7226 (mm-30) REVERT: B 295 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6849 (pt0) REVERT: B 313 GLN cc_start: 0.6718 (mp10) cc_final: 0.6371 (mp10) REVERT: B 415 MET cc_start: 0.8262 (tpp) cc_final: 0.7887 (mtt) REVERT: B 429 MET cc_start: 0.8619 (tmm) cc_final: 0.8203 (tmt) REVERT: B 486 ARG cc_start: 0.7307 (mtt90) cc_final: 0.7021 (mtt90) REVERT: B 540 ARG cc_start: 0.7508 (ttp-170) cc_final: 0.7124 (ttp80) REVERT: B 562 LYS cc_start: 0.7097 (OUTLIER) cc_final: 0.6584 (mptt) REVERT: B 565 GLU cc_start: 0.7315 (mt-10) cc_final: 0.6884 (mt-10) REVERT: B 595 THR cc_start: 0.8259 (OUTLIER) cc_final: 0.7963 (p) outliers start: 61 outliers final: 27 residues processed: 212 average time/residue: 1.5353 time to fit residues: 370.2332 Evaluate side-chains 209 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 167 time to evaluate : 2.395 ------------------------------------------------------------------------------- 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 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 330 LYS Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 462 LEU Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 530 ASP 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 268 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 78 optimal weight: 1.9990 chunk 205 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 174 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 140 optimal weight: 0.7980 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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** A 420 GLN C 414 ASN C 420 GLN ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 GLN B 420 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.215146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.144914 restraints weight = 17668.469| |-----------------------------------------------------------------------------| r_work (start): 0.3918 rms_B_bonded: 2.35 r_work: 0.3822 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3704 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17360 Z= 0.198 Angle : 0.612 10.399 23532 Z= 0.314 Chirality : 0.042 0.172 2652 Planarity : 0.004 0.066 2948 Dihedral : 5.092 29.513 2308 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 3.08 % Allowed : 16.90 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.18), residues: 2076 helix: 0.03 (0.15), residues: 1284 sheet: 0.19 (0.51), residues: 88 loop : -1.90 (0.20), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 574 HIS 0.004 0.001 HIS D 275 PHE 0.026 0.002 PHE C 103 TYR 0.015 0.002 TYR C 266 ARG 0.008 0.001 ARG D 527 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 820) hydrogen bonds : angle 4.52781 ( 2328) SS BOND : bond 0.00232 ( 12) SS BOND : angle 1.06165 ( 24) covalent geometry : bond 0.00473 (17348) covalent geometry : angle 0.61123 (23508) *********************** 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 219 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 162 time to evaluate : 2.042 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.5489 (mpp) cc_final: 0.4833 (mpp) REVERT: A 214 SER cc_start: 0.4181 (OUTLIER) cc_final: 0.3935 (t) REVERT: A 287 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7252 (mm-30) REVERT: A 315 MET cc_start: 0.7332 (mtt) cc_final: 0.7116 (mtp) REVERT: A 429 MET cc_start: 0.8596 (tmm) cc_final: 0.8209 (tmt) REVERT: A 486 ARG cc_start: 0.7362 (mtt90) cc_final: 0.7019 (mtt90) REVERT: A 540 ARG cc_start: 0.7647 (ttp-170) cc_final: 0.7117 (ttp80) REVERT: A 565 GLU cc_start: 0.7281 (mt-10) cc_final: 0.6851 (mt-10) REVERT: A 567 CYS cc_start: 0.6895 (OUTLIER) cc_final: 0.5365 (m) REVERT: C 155 MET cc_start: 0.5398 (mpp) cc_final: 0.4832 (mpp) REVERT: C 232 VAL cc_start: 0.6278 (m) cc_final: 0.6036 (p) REVERT: C 287 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7620 (mm-30) REVERT: C 295 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.7003 (pt0) REVERT: C 313 GLN cc_start: 0.6755 (mp10) cc_final: 0.6417 (mp10) REVERT: C 315 MET cc_start: 0.7348 (mtt) cc_final: 0.7108 (mtt) REVERT: C 330 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7304 (tppt) REVERT: C 392 MET cc_start: 0.7949 (tpt) cc_final: 0.7340 (ttt) REVERT: C 429 MET cc_start: 0.8566 (tmm) cc_final: 0.8196 (tmt) REVERT: C 486 ARG cc_start: 0.7425 (ttm170) cc_final: 0.6827 (ttm110) REVERT: C 565 GLU cc_start: 0.7332 (mt-10) cc_final: 0.6902 (mt-10) REVERT: D 155 MET cc_start: 0.5479 (mpp) cc_final: 0.4805 (mpp) REVERT: D 287 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7244 (mm-30) REVERT: D 313 GLN cc_start: 0.6760 (mp10) cc_final: 0.6425 (mp10) REVERT: D 415 MET cc_start: 0.8282 (tpp) cc_final: 0.7976 (mtp) REVERT: D 419 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8091 (mp) REVERT: D 429 MET cc_start: 0.8571 (tmm) cc_final: 0.8194 (tmt) REVERT: D 486 ARG cc_start: 0.7400 (mtt90) cc_final: 0.7076 (mtt90) REVERT: D 540 ARG cc_start: 0.7713 (ttp-170) cc_final: 0.7359 (ttp80) REVERT: D 562 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6614 (mptt) REVERT: D 565 GLU cc_start: 0.7371 (mt-10) cc_final: 0.6946 (mt-10) REVERT: B 155 MET cc_start: 0.5528 (mpp) cc_final: 0.4846 (mpp) REVERT: B 287 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7296 (mm-30) REVERT: B 313 GLN cc_start: 0.6729 (mp10) cc_final: 0.6378 (mp10) REVERT: B 415 MET cc_start: 0.8314 (tpp) cc_final: 0.7783 (mtt) REVERT: B 429 MET cc_start: 0.8577 (tmm) cc_final: 0.8194 (tmt) REVERT: B 486 ARG cc_start: 0.7354 (mtt90) cc_final: 0.7049 (mtt90) REVERT: B 527 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6555 (ptp-110) REVERT: B 540 ARG cc_start: 0.7721 (ttp-170) cc_final: 0.7327 (ttp80) REVERT: B 562 LYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6620 (mptt) REVERT: B 565 GLU cc_start: 0.7293 (mt-10) cc_final: 0.6884 (mt-10) outliers start: 57 outliers final: 34 residues processed: 198 average time/residue: 1.4613 time to fit residues: 324.0798 Evaluate side-chains 202 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 156 time to evaluate : 1.764 ------------------------------------------------------------------------------- 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 295 GLU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 530 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 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 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 419 LEU 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 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 527 ARG 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 193 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 22 optimal weight: 0.0060 chunk 162 optimal weight: 4.9990 chunk 6 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 chunk 121 optimal weight: 1.9990 chunk 163 optimal weight: 6.9990 chunk 204 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 195 optimal weight: 0.9990 overall best weight: 0.9802 ------------------------------------------------------------------------------- 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** A 420 GLN ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.216389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.146770 restraints weight = 17548.606| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.37 r_work: 0.3839 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3715 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17360 Z= 0.144 Angle : 0.562 9.013 23532 Z= 0.290 Chirality : 0.040 0.160 2652 Planarity : 0.004 0.059 2948 Dihedral : 4.949 28.658 2308 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 3.02 % Allowed : 17.06 % Favored : 79.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.18), residues: 2076 helix: 0.16 (0.16), residues: 1284 sheet: 0.50 (0.51), residues: 88 loop : -1.84 (0.20), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 574 HIS 0.004 0.001 HIS D 275 PHE 0.028 0.001 PHE C 103 TYR 0.011 0.002 TYR B 309 ARG 0.006 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.03119 ( 820) hydrogen bonds : angle 4.34850 ( 2328) SS BOND : bond 0.00160 ( 12) SS BOND : angle 0.84011 ( 24) covalent geometry : bond 0.00342 (17348) covalent geometry : angle 0.56152 (23508) *********************** 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: 56 poor density : 166 time to evaluate : 1.720 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.5297 (mpp) cc_final: 0.4642 (mpp) REVERT: A 214 SER cc_start: 0.4209 (OUTLIER) cc_final: 0.3983 (t) REVERT: A 287 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7056 (mm-30) REVERT: A 295 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.6740 (pt0) REVERT: A 315 MET cc_start: 0.7223 (mtt) cc_final: 0.7010 (mtp) REVERT: A 415 MET cc_start: 0.8159 (mtp) cc_final: 0.7623 (mtt) REVERT: A 419 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.8010 (mp) REVERT: A 429 MET cc_start: 0.8551 (tmm) cc_final: 0.8146 (tmt) REVERT: A 486 ARG cc_start: 0.7166 (mtt90) cc_final: 0.6867 (mtt90) REVERT: A 540 ARG cc_start: 0.7488 (ttp-170) cc_final: 0.6935 (ttp80) REVERT: A 565 GLU cc_start: 0.7302 (mt-10) cc_final: 0.6805 (mt-10) REVERT: A 595 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.7924 (p) REVERT: C 155 MET cc_start: 0.5347 (mpp) cc_final: 0.4740 (mpp) REVERT: C 232 VAL cc_start: 0.6263 (m) cc_final: 0.6008 (p) REVERT: C 287 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7451 (mm-30) REVERT: C 295 GLU cc_start: 0.6995 (OUTLIER) cc_final: 0.6761 (pt0) REVERT: C 313 GLN cc_start: 0.6612 (mp10) cc_final: 0.6282 (mp10) REVERT: C 330 LYS cc_start: 0.8292 (OUTLIER) cc_final: 0.7295 (tppt) REVERT: C 392 MET cc_start: 0.7855 (tpt) cc_final: 0.7223 (ttt) REVERT: C 415 MET cc_start: 0.8232 (mtp) cc_final: 0.7714 (mtt) REVERT: C 429 MET cc_start: 0.8533 (tmm) cc_final: 0.8139 (tmt) REVERT: C 486 ARG cc_start: 0.7286 (ttm170) cc_final: 0.6656 (ttm110) REVERT: C 565 GLU cc_start: 0.7380 (mt-10) cc_final: 0.6940 (mt-10) REVERT: D 155 MET cc_start: 0.5365 (mpp) cc_final: 0.4744 (mpp) REVERT: D 287 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7071 (mm-30) REVERT: D 313 GLN cc_start: 0.6629 (mp10) cc_final: 0.6315 (mp10) REVERT: D 415 MET cc_start: 0.8165 (tpp) cc_final: 0.7866 (mtp) REVERT: D 419 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7989 (mp) REVERT: D 429 MET cc_start: 0.8532 (tmm) cc_final: 0.8132 (tmt) REVERT: D 486 ARG cc_start: 0.7137 (mtt90) cc_final: 0.6853 (mtt90) REVERT: D 540 ARG cc_start: 0.7591 (ttp-170) cc_final: 0.7059 (ttp80) REVERT: D 562 LYS cc_start: 0.7030 (OUTLIER) cc_final: 0.6524 (mptt) REVERT: D 565 GLU cc_start: 0.7373 (mt-10) cc_final: 0.6940 (mt-10) REVERT: D 595 THR cc_start: 0.8135 (OUTLIER) cc_final: 0.7802 (p) REVERT: B 155 MET cc_start: 0.5361 (mpp) cc_final: 0.4719 (mpp) REVERT: B 287 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7114 (mm-30) REVERT: B 295 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6792 (pt0) REVERT: B 313 GLN cc_start: 0.6607 (mp10) cc_final: 0.6276 (mp10) REVERT: B 415 MET cc_start: 0.8185 (tpp) cc_final: 0.7943 (mtp) REVERT: B 429 MET cc_start: 0.8537 (tmm) cc_final: 0.8132 (tmt) REVERT: B 486 ARG cc_start: 0.7133 (mtt90) cc_final: 0.6842 (mtt90) REVERT: B 540 ARG cc_start: 0.7577 (ttp-170) cc_final: 0.7165 (ttp80) REVERT: B 562 LYS cc_start: 0.7037 (OUTLIER) cc_final: 0.6578 (mptt) REVERT: B 565 GLU cc_start: 0.7319 (mt-10) cc_final: 0.6892 (mt-10) outliers start: 56 outliers final: 28 residues processed: 204 average time/residue: 1.2376 time to fit residues: 282.4572 Evaluate side-chains 201 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 158 time to evaluate : 1.730 ------------------------------------------------------------------------------- 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 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 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 419 LEU Chi-restraints excluded: chain D residue 462 LEU Chi-restraints excluded: chain D residue 533 ASP 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 202 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 184 optimal weight: 1.9990 chunk 156 optimal weight: 20.0000 chunk 126 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 179 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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** A 420 GLN ** D 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 420 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.215899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.145633 restraints weight = 17646.000| |-----------------------------------------------------------------------------| r_work (start): 0.3921 rms_B_bonded: 2.35 r_work: 0.3823 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3702 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17360 Z= 0.159 Angle : 0.580 8.590 23532 Z= 0.299 Chirality : 0.041 0.165 2652 Planarity : 0.004 0.057 2948 Dihedral : 4.978 28.801 2308 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.65 % Allowed : 17.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.18), residues: 2076 helix: 0.15 (0.16), residues: 1288 sheet: 0.93 (0.60), residues: 48 loop : -1.76 (0.19), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 574 HIS 0.004 0.001 HIS A 275 PHE 0.030 0.001 PHE B 103 TYR 0.014 0.002 TYR D 266 ARG 0.009 0.000 ARG C 527 Details of bonding type rmsd hydrogen bonds : bond 0.03244 ( 820) hydrogen bonds : angle 4.40946 ( 2328) SS BOND : bond 0.00180 ( 12) SS BOND : angle 0.91928 ( 24) covalent geometry : bond 0.00376 (17348) covalent geometry : angle 0.57912 (23508) *********************** 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 208 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 159 time to evaluate : 1.712 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.5370 (mpp) cc_final: 0.4787 (mpp) REVERT: A 214 SER cc_start: 0.4264 (OUTLIER) cc_final: 0.4034 (t) REVERT: A 287 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7238 (mm-30) REVERT: A 415 MET cc_start: 0.8332 (mtp) cc_final: 0.7870 (mtt) REVERT: A 429 MET cc_start: 0.8619 (tmm) cc_final: 0.8232 (tmt) REVERT: A 486 ARG cc_start: 0.7283 (mtt90) cc_final: 0.6975 (mtt90) REVERT: A 540 ARG cc_start: 0.7650 (ttp-170) cc_final: 0.7097 (ttp80) REVERT: A 565 GLU cc_start: 0.7326 (mt-10) cc_final: 0.6872 (mt-10) REVERT: C 155 MET cc_start: 0.5211 (mpp) cc_final: 0.4658 (mpp) REVERT: C 232 VAL cc_start: 0.6177 (m) cc_final: 0.5949 (p) REVERT: C 287 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7617 (mm-30) REVERT: C 295 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6905 (pt0) REVERT: C 313 GLN cc_start: 0.6682 (mp10) cc_final: 0.6366 (mp10) REVERT: C 330 LYS cc_start: 0.8329 (OUTLIER) cc_final: 0.7335 (tppt) REVERT: C 392 MET cc_start: 0.7968 (tpt) cc_final: 0.7345 (ttt) REVERT: C 429 MET cc_start: 0.8592 (tmm) cc_final: 0.8218 (tmt) REVERT: C 486 ARG cc_start: 0.7447 (ttm170) cc_final: 0.7209 (mtt90) REVERT: C 565 GLU cc_start: 0.7310 (mt-10) cc_final: 0.6867 (mt-10) REVERT: C 567 CYS cc_start: 0.6731 (OUTLIER) cc_final: 0.5945 (t) REVERT: D 155 MET cc_start: 0.5391 (mpp) cc_final: 0.4725 (mpp) REVERT: D 287 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7235 (mm-30) REVERT: D 313 GLN cc_start: 0.6715 (mp10) cc_final: 0.6401 (mp10) REVERT: D 415 MET cc_start: 0.8293 (tpp) cc_final: 0.8007 (mtp) REVERT: D 419 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.8091 (mp) REVERT: D 429 MET cc_start: 0.8605 (tmm) cc_final: 0.8220 (tmt) REVERT: D 486 ARG cc_start: 0.7262 (mtt90) cc_final: 0.6973 (mtt90) REVERT: D 540 ARG cc_start: 0.7666 (ttp-170) cc_final: 0.7150 (ttp80) REVERT: D 562 LYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6555 (mptt) REVERT: D 565 GLU cc_start: 0.7365 (mt-10) cc_final: 0.6930 (mt-10) REVERT: B 155 MET cc_start: 0.5376 (mpp) cc_final: 0.4701 (mpp) REVERT: B 287 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7262 (mm-30) REVERT: B 295 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6966 (pt0) REVERT: B 313 GLN cc_start: 0.6688 (mp10) cc_final: 0.6363 (mp10) REVERT: B 415 MET cc_start: 0.8309 (tpp) cc_final: 0.8072 (mtp) REVERT: B 429 MET cc_start: 0.8604 (tmm) cc_final: 0.8218 (tmt) REVERT: B 486 ARG cc_start: 0.7258 (mtt90) cc_final: 0.6958 (mtt90) REVERT: B 540 ARG cc_start: 0.7669 (ttp-170) cc_final: 0.7276 (ttp80) REVERT: B 562 LYS cc_start: 0.7057 (OUTLIER) cc_final: 0.6582 (mptt) REVERT: B 565 GLU cc_start: 0.7245 (mt-10) cc_final: 0.6796 (mt-10) outliers start: 49 outliers final: 31 residues processed: 196 average time/residue: 1.2514 time to fit residues: 275.0594 Evaluate side-chains 196 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 153 time to evaluate : 1.878 ------------------------------------------------------------------------------- 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 520 THR 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 520 THR 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 419 LEU 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 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 47 optimal weight: 0.2980 chunk 7 optimal weight: 7.9990 chunk 78 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 36 optimal weight: 0.0570 chunk 5 optimal weight: 0.7980 chunk 107 optimal weight: 0.0970 chunk 181 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 55 optimal weight: 0.0670 chunk 11 optimal weight: 0.7980 overall best weight: 0.2634 ------------------------------------------------------------------------------- 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 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 = 0.4502 r_free = 0.4502 target = 0.220287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.151752 restraints weight = 17603.415| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 2.34 r_work: 0.3881 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3760 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 moved from start: 0.3337 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= 0.090 Angle : 0.516 7.889 23532 Z= 0.265 Chirality : 0.038 0.165 2652 Planarity : 0.003 0.055 2948 Dihedral : 4.639 27.928 2308 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.11 % Allowed : 18.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.19), residues: 2076 helix: 0.59 (0.16), residues: 1256 sheet: 0.63 (0.59), residues: 56 loop : -1.68 (0.20), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 281 HIS 0.003 0.001 HIS B 275 PHE 0.031 0.001 PHE C 103 TYR 0.008 0.001 TYR B 309 ARG 0.008 0.000 ARG C 527 Details of bonding type rmsd hydrogen bonds : bond 0.02542 ( 820) hydrogen bonds : angle 4.00943 ( 2328) SS BOND : bond 0.00112 ( 12) SS BOND : angle 0.57169 ( 24) covalent geometry : bond 0.00202 (17348) covalent geometry : angle 0.51594 (23508) ********************** 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 230 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 1.951 Fit side-chains revert: symmetry clash REVERT: A 155 MET cc_start: 0.5379 (mpp) cc_final: 0.4746 (mpp) REVERT: A 287 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7038 (mm-30) REVERT: A 313 GLN cc_start: 0.6593 (mp10) cc_final: 0.6255 (mp10) REVERT: A 330 LYS cc_start: 0.8331 (ttmm) cc_final: 0.7552 (tppt) REVERT: A 415 MET cc_start: 0.8094 (mtp) cc_final: 0.7579 (mtt) REVERT: A 429 MET cc_start: 0.8600 (tmm) cc_final: 0.8207 (tmt) REVERT: A 486 ARG cc_start: 0.7164 (mtt90) cc_final: 0.6939 (mtt90) REVERT: A 540 ARG cc_start: 0.7473 (ttp-170) cc_final: 0.7024 (ttp80) REVERT: A 565 GLU cc_start: 0.7519 (mt-10) cc_final: 0.7004 (mt-10) REVERT: A 595 THR cc_start: 0.8257 (OUTLIER) cc_final: 0.8019 (p) REVERT: C 155 MET cc_start: 0.5111 (mpp) cc_final: 0.4620 (mpp) REVERT: C 232 VAL cc_start: 0.6464 (m) cc_final: 0.6200 (p) REVERT: C 313 GLN cc_start: 0.6643 (mp10) cc_final: 0.6287 (mp10) REVERT: C 330 LYS cc_start: 0.8299 (OUTLIER) cc_final: 0.7379 (tppt) REVERT: C 392 MET cc_start: 0.7887 (tpt) cc_final: 0.7268 (ttt) REVERT: C 415 MET cc_start: 0.8105 (mtp) cc_final: 0.7630 (mtt) REVERT: C 429 MET cc_start: 0.8586 (tmm) cc_final: 0.8198 (tmt) REVERT: C 486 ARG cc_start: 0.7295 (ttm170) cc_final: 0.6712 (ttm110) REVERT: C 565 GLU cc_start: 0.7473 (mt-10) cc_final: 0.7016 (mt-10) REVERT: C 595 THR cc_start: 0.8353 (OUTLIER) cc_final: 0.8082 (p) REVERT: D 155 MET cc_start: 0.5425 (mpp) cc_final: 0.4824 (mpp) REVERT: D 287 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7075 (mm-30) REVERT: D 313 GLN cc_start: 0.6597 (mp10) cc_final: 0.6292 (mp10) REVERT: D 330 LYS cc_start: 0.8334 (ttmm) cc_final: 0.7619 (tppt) REVERT: D 415 MET cc_start: 0.8188 (tpp) cc_final: 0.7914 (mtp) REVERT: D 429 MET cc_start: 0.8591 (tmm) cc_final: 0.8201 (tmt) REVERT: D 540 ARG cc_start: 0.7419 (ttp-170) cc_final: 0.7043 (ttp80) REVERT: D 565 GLU cc_start: 0.7491 (mt-10) cc_final: 0.7198 (mt-10) REVERT: D 566 PHE cc_start: 0.7952 (p90) cc_final: 0.7670 (p90) REVERT: D 567 CYS cc_start: 0.6539 (t) cc_final: 0.5274 (m) REVERT: D 594 LEU cc_start: 0.8451 (mt) cc_final: 0.8229 (mt) REVERT: D 595 THR cc_start: 0.8226 (OUTLIER) cc_final: 0.8008 (p) REVERT: B 155 MET cc_start: 0.5473 (mpp) cc_final: 0.4836 (mpp) REVERT: B 270 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.6346 (t80) REVERT: B 287 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7078 (mm-30) REVERT: B 313 GLN cc_start: 0.6626 (mp10) cc_final: 0.6332 (mp10) REVERT: B 330 LYS cc_start: 0.8425 (ttmm) cc_final: 0.7711 (tppt) REVERT: B 415 MET cc_start: 0.8200 (tpp) cc_final: 0.7932 (mtp) REVERT: B 429 MET cc_start: 0.8619 (tmm) cc_final: 0.8223 (tmt) REVERT: B 540 ARG cc_start: 0.7406 (ttp-170) cc_final: 0.7004 (ttp80) REVERT: B 562 LYS cc_start: 0.6942 (OUTLIER) cc_final: 0.6537 (mptt) REVERT: B 565 GLU cc_start: 0.7407 (mt-10) cc_final: 0.7002 (mt-10) REVERT: B 567 CYS cc_start: 0.6450 (t) cc_final: 0.6183 (t) REVERT: B 594 LEU cc_start: 0.8384 (mt) cc_final: 0.8181 (mm) REVERT: B 595 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8075 (p) outliers start: 39 outliers final: 21 residues processed: 218 average time/residue: 1.2159 time to fit residues: 298.0988 Evaluate side-chains 211 residues out of total 1852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 180 time to evaluate : 1.828 ------------------------------------------------------------------------------- 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 508 ASP Chi-restraints excluded: chain A residue 520 THR Chi-restraints excluded: chain A residue 567 CYS Chi-restraints excluded: chain A residue 594 LEU Chi-restraints excluded: chain A residue 595 THR Chi-restraints excluded: chain C residue 234 TYR Chi-restraints excluded: chain C residue 297 CYS Chi-restraints excluded: chain C residue 330 LYS Chi-restraints excluded: chain C residue 507 LEU Chi-restraints excluded: chain C residue 520 THR Chi-restraints excluded: chain C residue 567 CYS Chi-restraints excluded: chain C residue 595 THR Chi-restraints excluded: chain D residue 229 ILE 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 508 ASP Chi-restraints excluded: chain D residue 595 THR Chi-restraints excluded: chain B residue 229 ILE 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 508 ASP 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 22 optimal weight: 0.2980 chunk 202 optimal weight: 0.2980 chunk 30 optimal weight: 0.5980 chunk 132 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 3 optimal weight: 0.0010 chunk 26 optimal weight: 2.9990 chunk 174 optimal weight: 0.5980 chunk 60 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 overall best weight: 0.3586 ------------------------------------------------------------------------------- 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 233 GLN ** D 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 = 0.4501 r_free = 0.4501 target = 0.220386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.151511 restraints weight = 17627.439| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 2.33 r_work: 0.3867 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3745 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 17360 Z= 0.095 Angle : 0.517 7.150 23532 Z= 0.265 Chirality : 0.038 0.165 2652 Planarity : 0.003 0.054 2948 Dihedral : 4.543 27.717 2308 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 1.78 % Allowed : 19.01 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.19), residues: 2076 helix: 0.68 (0.16), residues: 1256 sheet: 0.81 (0.48), residues: 96 loop : -1.63 (0.20), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 281 HIS 0.004 0.001 HIS D 275 PHE 0.029 0.001 PHE C 103 TYR 0.008 0.001 TYR C 270 ARG 0.008 0.000 ARG C 527 Details of bonding type rmsd hydrogen bonds : bond 0.02618 ( 820) hydrogen bonds : angle 3.98627 ( 2328) SS BOND : bond 0.00082 ( 12) SS BOND : angle 0.61546 ( 24) covalent geometry : bond 0.00213 (17348) covalent geometry : angle 0.51659 (23508) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16625.16 seconds wall clock time: 291 minutes 44.36 seconds (17504.36 seconds total)