Starting phenix.real_space_refine on Thu Mar 5 04:39:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t38_25651/03_2026/7t38_25651.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t38_25651/03_2026/7t38_25651.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t38_25651/03_2026/7t38_25651.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t38_25651/03_2026/7t38_25651.map" model { file = "/net/cci-nas-00/data/ceres_data/7t38_25651/03_2026/7t38_25651.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t38_25651/03_2026/7t38_25651.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.016 sd= 0.056 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 112 5.16 5 C 12736 2.51 5 N 3256 2.21 5 O 3300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19404 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 608, 4851 Classifications: {'peptide': 608} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 586} Chain breaks: 4 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 81 Planarities with less than four sites: {'ARG:plan': 5, 'ASP:plan': 3, 'GLU:plan': 14} Unresolved non-hydrogen planarities: 90 Restraints were copied for chains: B, C, D Time building chain proxies: 4.39, per 1000 atoms: 0.23 Number of scatterers: 19404 At special positions: 0 Unit cell: (144.45, 144.45, 115.56, 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 112 16.00 O 3300 8.00 N 3256 7.00 C 12736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 765.4 milliseconds 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4592 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 8 sheets defined 62.5% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.505A pdb=" N GLY A 87 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 93 removed outlier: 3.706A pdb=" N THR A 93 " --> pdb=" O GLU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 103 Processing helix chain 'A' and resid 108 through 112 Processing helix chain 'A' and resid 119 through 127 removed outlier: 3.643A pdb=" N LYS A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 147 removed outlier: 3.565A pdb=" N GLY A 147 " --> pdb=" O ASP A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 174 removed outlier: 3.532A pdb=" N ILE A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 212 through 220 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.738A pdb=" N LEU A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 removed outlier: 3.782A pdb=" N ILE A 290 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 306 removed outlier: 3.567A pdb=" N GLY A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.762A pdb=" N HIS A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 362 Processing helix chain 'A' and resid 370 through 375 removed outlier: 4.018A pdb=" N VAL A 374 " --> pdb=" O HIS A 370 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU A 375 " --> pdb=" O ARG A 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 370 through 375' Processing helix chain 'A' and resid 377 through 413 removed outlier: 5.346A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 467 through 469 No H-bonds generated for 'chain 'A' and resid 467 through 469' Processing helix chain 'A' and resid 470 through 492 Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.953A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 removed outlier: 3.573A pdb=" N THR A 516 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 517' Processing helix chain 'A' and resid 521 through 534 removed outlier: 3.991A pdb=" N TYR A 525 " --> pdb=" O HIS A 521 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET A 528 " --> pdb=" O ILE A 524 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE A 529 " --> pdb=" O TYR A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 558 removed outlier: 4.258A pdb=" N LEU A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY A 550 " --> pdb=" O VAL A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 602 Processing helix chain 'A' and resid 618 through 649 removed outlier: 3.978A pdb=" N LEU A 638 " --> pdb=" O TYR A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 673 removed outlier: 3.945A pdb=" N SER A 656 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN A 673 " --> pdb=" O LEU A 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.505A pdb=" N GLY B 87 " --> pdb=" O VAL B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 93 removed outlier: 3.707A pdb=" N THR B 93 " --> pdb=" O GLU B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 94 through 103 Processing helix chain 'B' and resid 108 through 112 Processing helix chain 'B' and resid 119 through 127 removed outlier: 3.642A pdb=" N LYS B 123 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 147 removed outlier: 3.565A pdb=" N GLY B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 174 removed outlier: 3.532A pdb=" N ILE B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 185 Processing helix chain 'B' and resid 212 through 220 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.738A pdb=" N LEU B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 removed outlier: 3.782A pdb=" N ILE B 290 " --> pdb=" O LEU B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 306 removed outlier: 3.567A pdb=" N GLY B 306 " --> pdb=" O ALA B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.762A pdb=" N HIS B 313 " --> pdb=" O GLU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 370 through 375 removed outlier: 4.018A pdb=" N VAL B 374 " --> pdb=" O HIS B 370 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU B 375 " --> pdb=" O ARG B 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 370 through 375' Processing helix chain 'B' and resid 377 through 413 removed outlier: 5.346A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 467 through 469 No H-bonds generated for 'chain 'B' and resid 467 through 469' Processing helix chain 'B' and resid 470 through 492 Processing helix chain 'B' and resid 496 through 512 removed outlier: 3.953A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.573A pdb=" N THR B 516 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 513 through 517' Processing helix chain 'B' and resid 521 through 534 removed outlier: 3.991A pdb=" N TYR B 525 " --> pdb=" O HIS B 521 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET B 528 " --> pdb=" O ILE B 524 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE B 529 " --> pdb=" O TYR B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 536 through 558 removed outlier: 4.259A pdb=" N LEU B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY B 550 " --> pdb=" O VAL B 546 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 602 Processing helix chain 'B' and resid 618 through 649 removed outlier: 3.979A pdb=" N LEU B 638 " --> pdb=" O TYR B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 673 removed outlier: 3.944A pdb=" N SER B 656 " --> pdb=" O VAL B 652 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN B 673 " --> pdb=" O LEU B 669 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.504A pdb=" N GLY C 87 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 93 removed outlier: 3.707A pdb=" N THR C 93 " --> pdb=" O GLU C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 103 Processing helix chain 'C' and resid 108 through 112 Processing helix chain 'C' and resid 119 through 127 removed outlier: 3.642A pdb=" N LYS C 123 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 147 removed outlier: 3.566A pdb=" N GLY C 147 " --> pdb=" O ASP C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 174 removed outlier: 3.532A pdb=" N ILE C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 185 Processing helix chain 'C' and resid 212 through 220 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.738A pdb=" N LEU C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 removed outlier: 3.782A pdb=" N ILE C 290 " --> pdb=" O LEU C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 306 removed outlier: 3.567A pdb=" N GLY C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.763A pdb=" N HIS C 313 " --> pdb=" O GLU C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 362 Processing helix chain 'C' and resid 370 through 375 removed outlier: 4.018A pdb=" N VAL C 374 " --> pdb=" O HIS C 370 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU C 375 " --> pdb=" O ARG C 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 370 through 375' Processing helix chain 'C' and resid 377 through 413 removed outlier: 5.346A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 467 through 469 No H-bonds generated for 'chain 'C' and resid 467 through 469' Processing helix chain 'C' and resid 470 through 492 Processing helix chain 'C' and resid 496 through 512 removed outlier: 3.954A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 517 removed outlier: 3.573A pdb=" N THR C 516 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 513 through 517' Processing helix chain 'C' and resid 521 through 534 removed outlier: 3.991A pdb=" N TYR C 525 " --> pdb=" O HIS C 521 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET C 528 " --> pdb=" O ILE C 524 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE C 529 " --> pdb=" O TYR C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 558 removed outlier: 4.259A pdb=" N LEU C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY C 550 " --> pdb=" O VAL C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 602 Processing helix chain 'C' and resid 618 through 649 removed outlier: 3.979A pdb=" N LEU C 638 " --> pdb=" O TYR C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 673 removed outlier: 3.944A pdb=" N SER C 656 " --> pdb=" O VAL C 652 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN C 673 " --> pdb=" O LEU C 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 87 removed outlier: 3.505A pdb=" N GLY D 87 " --> pdb=" O VAL D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 93 removed outlier: 3.707A pdb=" N THR D 93 " --> pdb=" O GLU D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 103 Processing helix chain 'D' and resid 108 through 112 Processing helix chain 'D' and resid 119 through 127 removed outlier: 3.643A pdb=" N LYS D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 147 removed outlier: 3.565A pdb=" N GLY D 147 " --> pdb=" O ASP D 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 174 removed outlier: 3.532A pdb=" N ILE D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 185 Processing helix chain 'D' and resid 212 through 220 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.738A pdb=" N LEU D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 removed outlier: 3.783A pdb=" N ILE D 290 " --> pdb=" O LEU D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 306 removed outlier: 3.567A pdb=" N GLY D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.762A pdb=" N HIS D 313 " --> pdb=" O GLU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 362 Processing helix chain 'D' and resid 370 through 375 removed outlier: 4.018A pdb=" N VAL D 374 " --> pdb=" O HIS D 370 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU D 375 " --> pdb=" O ARG D 371 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 370 through 375' Processing helix chain 'D' and resid 377 through 413 removed outlier: 5.346A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 467 through 469 No H-bonds generated for 'chain 'D' and resid 467 through 469' Processing helix chain 'D' and resid 470 through 492 Processing helix chain 'D' and resid 496 through 512 removed outlier: 3.953A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 517 removed outlier: 3.573A pdb=" N THR D 516 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 513 through 517' Processing helix chain 'D' and resid 521 through 534 removed outlier: 3.991A pdb=" N TYR D 525 " --> pdb=" O HIS D 521 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N MET D 528 " --> pdb=" O ILE D 524 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ILE D 529 " --> pdb=" O TYR D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 536 through 558 removed outlier: 4.259A pdb=" N LEU D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLY D 550 " --> pdb=" O VAL D 546 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 602 Processing helix chain 'D' and resid 618 through 649 removed outlier: 3.978A pdb=" N LEU D 638 " --> pdb=" O TYR D 634 " (cutoff:3.500A) Processing helix chain 'D' and resid 652 through 673 removed outlier: 3.944A pdb=" N SER D 656 " --> pdb=" O VAL D 652 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ASN D 673 " --> pdb=" O LEU D 669 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 157 through 158 Processing sheet with id=AA2, first strand: chain 'A' and resid 329 through 335 removed outlier: 7.533A pdb=" N LYS A 329 " --> pdb=" O ASP A 344 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ASP A 344 " --> pdb=" O LYS A 329 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR A 331 " --> pdb=" O LEU A 342 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU A 342 " --> pdb=" O THR A 331 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP A 333 " --> pdb=" O VAL A 340 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 338 " --> pdb=" O TYR A 335 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 702 " --> pdb=" O LEU A 689 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU A 689 " --> pdb=" O ARG A 702 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AA4, first strand: chain 'B' and resid 329 through 335 removed outlier: 7.534A pdb=" N LYS B 329 " --> pdb=" O ASP B 344 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ASP B 344 " --> pdb=" O LYS B 329 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR B 331 " --> pdb=" O LEU B 342 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU B 342 " --> pdb=" O THR B 331 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP B 333 " --> pdb=" O VAL B 340 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL B 338 " --> pdb=" O TYR B 335 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B 702 " --> pdb=" O LEU B 689 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 689 " --> pdb=" O ARG B 702 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 157 through 158 Processing sheet with id=AA6, first strand: chain 'C' and resid 329 through 335 removed outlier: 7.533A pdb=" N LYS C 329 " --> pdb=" O ASP C 344 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ASP C 344 " --> pdb=" O LYS C 329 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N THR C 331 " --> pdb=" O LEU C 342 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU C 342 " --> pdb=" O THR C 331 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TRP C 333 " --> pdb=" O VAL C 340 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL C 338 " --> pdb=" O TYR C 335 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG C 702 " --> pdb=" O LEU C 689 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 689 " --> pdb=" O ARG C 702 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 157 through 158 Processing sheet with id=AA8, first strand: chain 'D' and resid 329 through 335 removed outlier: 7.533A pdb=" N LYS D 329 " --> pdb=" O ASP D 344 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ASP D 344 " --> pdb=" O LYS D 329 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N THR D 331 " --> pdb=" O LEU D 342 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N LEU D 342 " --> pdb=" O THR D 331 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N TRP D 333 " --> pdb=" O VAL D 340 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N VAL D 338 " --> pdb=" O TYR D 335 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG D 702 " --> pdb=" O LEU D 689 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU D 689 " --> pdb=" O ARG D 702 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 3060 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: 3.11 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5977 1.34 - 1.46: 4821 1.46 - 1.58: 8922 1.58 - 1.70: 0 1.70 - 1.82: 172 Bond restraints: 19892 Sorted by residual: bond pdb=" C PRO D 325 " pdb=" N LEU D 326 " ideal model delta sigma weight residual 1.330 1.263 0.067 1.20e-02 6.94e+03 3.08e+01 bond pdb=" C PRO C 325 " pdb=" N LEU C 326 " ideal model delta sigma weight residual 1.330 1.263 0.066 1.20e-02 6.94e+03 3.06e+01 bond pdb=" C PRO A 325 " pdb=" N LEU A 326 " ideal model delta sigma weight residual 1.330 1.263 0.066 1.20e-02 6.94e+03 3.06e+01 bond pdb=" C PRO B 325 " pdb=" N LEU B 326 " ideal model delta sigma weight residual 1.330 1.263 0.066 1.20e-02 6.94e+03 3.06e+01 bond pdb=" C ARG B 539 " pdb=" N PHE B 540 " ideal model delta sigma weight residual 1.335 1.393 -0.058 1.31e-02 5.83e+03 1.98e+01 ... (remaining 19887 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 26154 1.93 - 3.85: 695 3.85 - 5.78: 95 5.78 - 7.71: 60 7.71 - 9.63: 12 Bond angle restraints: 27016 Sorted by residual: angle pdb=" C GLN B 520 " pdb=" CA GLN B 520 " pdb=" CB GLN B 520 " ideal model delta sigma weight residual 116.54 110.61 5.93 1.15e+00 7.56e-01 2.66e+01 angle pdb=" C GLN C 520 " pdb=" CA GLN C 520 " pdb=" CB GLN C 520 " ideal model delta sigma weight residual 116.54 110.64 5.90 1.15e+00 7.56e-01 2.63e+01 angle pdb=" C GLN A 520 " pdb=" CA GLN A 520 " pdb=" CB GLN A 520 " ideal model delta sigma weight residual 116.54 110.66 5.88 1.15e+00 7.56e-01 2.61e+01 angle pdb=" C GLN D 520 " pdb=" CA GLN D 520 " pdb=" CB GLN D 520 " ideal model delta sigma weight residual 116.54 110.70 5.84 1.15e+00 7.56e-01 2.58e+01 angle pdb=" N LEU A 296 " pdb=" CA LEU A 296 " pdb=" C LEU A 296 " ideal model delta sigma weight residual 110.42 116.83 -6.41 1.55e+00 4.16e-01 1.71e+01 ... (remaining 27011 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 10576 17.99 - 35.99: 896 35.99 - 53.98: 132 53.98 - 71.98: 24 71.98 - 89.97: 8 Dihedral angle restraints: 11636 sinusoidal: 4532 harmonic: 7104 Sorted by residual: dihedral pdb=" CA VAL D 546 " pdb=" C VAL D 546 " pdb=" N PHE D 547 " pdb=" CA PHE D 547 " ideal model delta harmonic sigma weight residual 180.00 158.80 21.20 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA VAL C 546 " pdb=" C VAL C 546 " pdb=" N PHE C 547 " pdb=" CA PHE C 547 " ideal model delta harmonic sigma weight residual 180.00 158.80 21.20 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA VAL B 546 " pdb=" C VAL B 546 " pdb=" N PHE B 547 " pdb=" CA PHE B 547 " ideal model delta harmonic sigma weight residual 180.00 158.80 21.20 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 11633 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2508 0.055 - 0.110: 534 0.110 - 0.164: 42 0.164 - 0.219: 4 0.219 - 0.274: 4 Chirality restraints: 3092 Sorted by residual: chirality pdb=" CB VAL C 546 " pdb=" CA VAL C 546 " pdb=" CG1 VAL C 546 " pdb=" CG2 VAL C 546 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB VAL D 546 " pdb=" CA VAL D 546 " pdb=" CG1 VAL D 546 " pdb=" CG2 VAL D 546 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.86e+00 chirality pdb=" CB VAL B 546 " pdb=" CA VAL B 546 " pdb=" CG1 VAL B 546 " pdb=" CG2 VAL B 546 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 3089 not shown) Planarity restraints: 3316 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 556 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" C VAL B 556 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL B 556 " 0.017 2.00e-02 2.50e+03 pdb=" N SER B 557 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 556 " -0.013 2.00e-02 2.50e+03 2.54e-02 6.47e+00 pdb=" C VAL C 556 " 0.044 2.00e-02 2.50e+03 pdb=" O VAL C 556 " -0.017 2.00e-02 2.50e+03 pdb=" N SER C 557 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 556 " 0.013 2.00e-02 2.50e+03 2.53e-02 6.41e+00 pdb=" C VAL A 556 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL A 556 " 0.016 2.00e-02 2.50e+03 pdb=" N SER A 557 " 0.015 2.00e-02 2.50e+03 ... (remaining 3313 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 6038 2.84 - 3.35: 18083 3.35 - 3.87: 31097 3.87 - 4.38: 32953 4.38 - 4.90: 58711 Nonbonded interactions: 146882 Sorted by model distance: nonbonded pdb=" OH TYR B 544 " pdb=" OG1 THR B 604 " model vdw 2.319 3.040 nonbonded pdb=" OH TYR C 544 " pdb=" OG1 THR C 604 " model vdw 2.320 3.040 nonbonded pdb=" OH TYR D 544 " pdb=" OG1 THR D 604 " model vdw 2.320 3.040 nonbonded pdb=" OH TYR A 544 " pdb=" OG1 THR A 604 " model vdw 2.320 3.040 nonbonded pdb=" O PHE A 209 " pdb=" OG SER A 215 " model vdw 2.326 3.040 ... (remaining 146877 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.270 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: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.260 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 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 : 0.004 0.067 19892 Z= 0.203 Angle : 0.777 9.631 27016 Z= 0.403 Chirality : 0.044 0.274 3092 Planarity : 0.005 0.062 3316 Dihedral : 13.601 89.971 7044 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.39 % Allowed : 0.92 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.24 (0.15), residues: 2392 helix: -0.02 (0.13), residues: 1424 sheet: 0.04 (0.44), residues: 64 loop : -2.16 (0.16), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 617 TYR 0.034 0.002 TYR D 525 PHE 0.016 0.001 PHE D 407 TRP 0.006 0.001 TRP C 333 HIS 0.003 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00355 (19892) covalent geometry : angle 0.77692 (27016) hydrogen bonds : bond 0.17023 ( 1044) hydrogen bonds : angle 5.17740 ( 3060) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 211 time to evaluate : 0.527 Fit side-chains REVERT: A 122 MET cc_start: 0.8573 (mtm) cc_final: 0.8113 (mtm) REVERT: A 141 GLN cc_start: 0.8579 (mm-40) cc_final: 0.7949 (tp-100) REVERT: A 162 TYR cc_start: 0.8050 (p90) cc_final: 0.7649 (p90) REVERT: B 122 MET cc_start: 0.8575 (mtm) cc_final: 0.8126 (mtm) REVERT: B 141 GLN cc_start: 0.8542 (mm-40) cc_final: 0.7919 (tp-100) REVERT: B 162 TYR cc_start: 0.8036 (p90) cc_final: 0.7613 (p90) REVERT: C 122 MET cc_start: 0.8573 (mtm) cc_final: 0.8123 (mtm) REVERT: C 141 GLN cc_start: 0.8548 (mm-40) cc_final: 0.7921 (tp-100) REVERT: C 162 TYR cc_start: 0.8040 (p90) cc_final: 0.7616 (p90) REVERT: D 122 MET cc_start: 0.8563 (mtm) cc_final: 0.8122 (mtm) REVERT: D 141 GLN cc_start: 0.8509 (mm-40) cc_final: 0.7886 (tp-100) REVERT: D 162 TYR cc_start: 0.8043 (p90) cc_final: 0.7622 (p90) REVERT: D 243 ASP cc_start: 0.8151 (p0) cc_final: 0.7946 (p0) outliers start: 8 outliers final: 0 residues processed: 211 average time/residue: 0.1120 time to fit residues: 39.2559 Evaluate side-chains 155 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.1980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 235 optimal weight: 0.8980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 511 ASN B 511 ASN C 511 ASN D 511 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.120312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.095431 restraints weight = 34380.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.097845 restraints weight = 22829.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.099508 restraints weight = 17647.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.100573 restraints weight = 14789.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.101383 restraints weight = 13138.343| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19892 Z= 0.132 Angle : 0.533 8.066 27016 Z= 0.261 Chirality : 0.037 0.122 3092 Planarity : 0.004 0.051 3316 Dihedral : 3.469 14.579 2632 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.93 % Allowed : 7.45 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.17), residues: 2392 helix: 1.20 (0.14), residues: 1436 sheet: 0.64 (0.54), residues: 64 loop : -1.97 (0.17), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 617 TYR 0.011 0.001 TYR A 162 PHE 0.011 0.001 PHE C 407 TRP 0.004 0.001 TRP B 677 HIS 0.002 0.001 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00302 (19892) covalent geometry : angle 0.53288 (27016) hydrogen bonds : bond 0.03604 ( 1044) hydrogen bonds : angle 3.40396 ( 3060) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 178 time to evaluate : 0.652 Fit side-chains REVERT: A 141 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8002 (tp-100) REVERT: A 211 GLU cc_start: 0.7935 (pm20) cc_final: 0.7460 (pm20) REVERT: B 141 GLN cc_start: 0.8572 (mm-40) cc_final: 0.7984 (tp-100) REVERT: B 211 GLU cc_start: 0.7936 (pm20) cc_final: 0.7464 (pm20) REVERT: C 141 GLN cc_start: 0.8564 (mm-40) cc_final: 0.7983 (tp-100) REVERT: D 141 GLN cc_start: 0.8562 (mm-40) cc_final: 0.7983 (tp-100) outliers start: 40 outliers final: 28 residues processed: 202 average time/residue: 0.1119 time to fit residues: 38.1788 Evaluate side-chains 179 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 151 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 683 HIS Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 683 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 199 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 174 optimal weight: 0.8980 chunk 239 optimal weight: 8.9990 chunk 177 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 228 optimal weight: 0.6980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 511 ASN D 511 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.119617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.094527 restraints weight = 35124.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.096928 restraints weight = 23800.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.098559 restraints weight = 18516.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.099603 restraints weight = 15633.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.100214 restraints weight = 13981.732| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 19892 Z= 0.124 Angle : 0.494 6.741 27016 Z= 0.247 Chirality : 0.037 0.123 3092 Planarity : 0.003 0.050 3316 Dihedral : 3.305 12.772 2632 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.84 % Allowed : 11.03 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.17), residues: 2392 helix: 1.77 (0.14), residues: 1440 sheet: 0.68 (0.55), residues: 64 loop : -1.85 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 617 TYR 0.030 0.001 TYR A 162 PHE 0.011 0.001 PHE A 407 TRP 0.004 0.001 TRP A 712 HIS 0.003 0.001 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00289 (19892) covalent geometry : angle 0.49431 (27016) hydrogen bonds : bond 0.03339 ( 1044) hydrogen bonds : angle 3.15846 ( 3060) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 147 time to evaluate : 0.716 Fit side-chains REVERT: A 141 GLN cc_start: 0.8640 (mm-40) cc_final: 0.7860 (tp-100) REVERT: A 645 MET cc_start: 0.7828 (tpp) cc_final: 0.7417 (tpp) REVERT: B 141 GLN cc_start: 0.8633 (mm-40) cc_final: 0.7853 (tp-100) REVERT: C 141 GLN cc_start: 0.8627 (mm-40) cc_final: 0.7851 (tp-100) REVERT: D 141 GLN cc_start: 0.8622 (mm-40) cc_final: 0.7850 (tp-100) outliers start: 38 outliers final: 28 residues processed: 173 average time/residue: 0.1187 time to fit residues: 34.5209 Evaluate side-chains 169 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 683 HIS Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 547 PHE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 683 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 170 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 138 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 125 optimal weight: 9.9990 chunk 180 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 165 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 ASN A 511 ASN B 186 ASN B 511 ASN C 186 ASN D 186 ASN D 511 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.119647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.094620 restraints weight = 35099.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.097054 restraints weight = 23556.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098678 restraints weight = 18202.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.099845 restraints weight = 15328.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.100450 restraints weight = 13622.659| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 19892 Z= 0.111 Angle : 0.480 7.289 27016 Z= 0.238 Chirality : 0.036 0.119 3092 Planarity : 0.003 0.050 3316 Dihedral : 3.197 12.455 2632 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.61 % Allowed : 12.77 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.17), residues: 2392 helix: 2.07 (0.14), residues: 1440 sheet: 0.85 (0.56), residues: 64 loop : -1.74 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 617 TYR 0.027 0.001 TYR A 162 PHE 0.009 0.001 PHE A 407 TRP 0.006 0.001 TRP C 223 HIS 0.003 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00259 (19892) covalent geometry : angle 0.48015 (27016) hydrogen bonds : bond 0.03118 ( 1044) hydrogen bonds : angle 3.00020 ( 3060) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 158 time to evaluate : 0.537 Fit side-chains REVERT: A 141 GLN cc_start: 0.8571 (mm-40) cc_final: 0.7971 (tp-100) REVERT: A 211 GLU cc_start: 0.7947 (pm20) cc_final: 0.7458 (pm20) REVERT: A 243 ASP cc_start: 0.7870 (p0) cc_final: 0.7659 (p0) REVERT: A 277 MET cc_start: 0.8362 (OUTLIER) cc_final: 0.7587 (mpp) REVERT: A 528 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6705 (ttm) REVERT: A 645 MET cc_start: 0.7844 (tpp) cc_final: 0.7582 (tpp) REVERT: B 141 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8043 (tp-100) REVERT: B 277 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7589 (mpp) REVERT: B 528 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6698 (ttm) REVERT: C 141 GLN cc_start: 0.8559 (mm-40) cc_final: 0.7962 (tp-100) REVERT: C 277 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7567 (mpp) REVERT: C 528 MET cc_start: 0.6993 (OUTLIER) cc_final: 0.6705 (ttm) REVERT: D 141 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8056 (tp-100) REVERT: D 277 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7575 (mpp) REVERT: D 528 MET cc_start: 0.6992 (OUTLIER) cc_final: 0.6681 (ttm) outliers start: 54 outliers final: 32 residues processed: 188 average time/residue: 0.1157 time to fit residues: 36.6063 Evaluate side-chains 189 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 528 MET Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain A residue 683 HIS Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 436 LEU Chi-restraints excluded: chain B residue 528 MET Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain B residue 683 HIS Chi-restraints excluded: chain C residue 151 LEU Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 436 LEU Chi-restraints excluded: chain C residue 528 MET Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 547 PHE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain D residue 151 LEU Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 528 MET Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 648 THR Chi-restraints excluded: chain D residue 683 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 43 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 161 optimal weight: 3.9990 chunk 12 optimal weight: 8.9990 chunk 221 optimal weight: 0.7980 chunk 193 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 169 optimal weight: 5.9990 chunk 218 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 511 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.116908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.091841 restraints weight = 35072.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.094203 restraints weight = 23774.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.095804 restraints weight = 18512.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.096844 restraints weight = 15697.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.097416 restraints weight = 14061.108| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 19892 Z= 0.156 Angle : 0.524 7.367 27016 Z= 0.258 Chirality : 0.038 0.123 3092 Planarity : 0.003 0.050 3316 Dihedral : 3.329 13.465 2632 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.93 % Allowed : 14.89 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.17), residues: 2392 helix: 2.03 (0.14), residues: 1448 sheet: 0.73 (0.56), residues: 64 loop : -1.71 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 706 TYR 0.017 0.001 TYR A 162 PHE 0.011 0.001 PHE A 407 TRP 0.007 0.001 TRP B 223 HIS 0.003 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00375 (19892) covalent geometry : angle 0.52417 (27016) hydrogen bonds : bond 0.03462 ( 1044) hydrogen bonds : angle 3.18785 ( 3060) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.688 Fit side-chains REVERT: A 141 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8026 (tp-100) REVERT: A 277 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.7655 (mpp) REVERT: A 645 MET cc_start: 0.7875 (tpp) cc_final: 0.7642 (tpp) REVERT: B 141 GLN cc_start: 0.8559 (mm-40) cc_final: 0.7963 (tp-100) REVERT: B 277 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7649 (mpp) REVERT: C 141 GLN cc_start: 0.8564 (mm-40) cc_final: 0.7970 (tp-100) REVERT: C 277 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.7639 (mpp) REVERT: D 141 GLN cc_start: 0.8556 (mm-40) cc_final: 0.7966 (tp-100) REVERT: D 277 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.7642 (mpp) outliers start: 40 outliers final: 31 residues processed: 191 average time/residue: 0.1109 time to fit residues: 35.6282 Evaluate side-chains 183 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 547 PHE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 648 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 163 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 199 optimal weight: 0.9990 chunk 94 optimal weight: 9.9990 chunk 235 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 165 optimal weight: 3.9990 chunk 125 optimal weight: 4.9990 chunk 224 optimal weight: 8.9990 chunk 205 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.117641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.092759 restraints weight = 34712.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.095167 restraints weight = 23361.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.096791 restraints weight = 18100.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.097856 restraints weight = 15270.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098496 restraints weight = 13634.397| |-----------------------------------------------------------------------------| r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 19892 Z= 0.126 Angle : 0.510 8.789 27016 Z= 0.247 Chirality : 0.037 0.121 3092 Planarity : 0.003 0.048 3316 Dihedral : 3.274 13.510 2632 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.93 % Allowed : 16.01 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.17), residues: 2392 helix: 2.18 (0.14), residues: 1440 sheet: 0.31 (0.55), residues: 64 loop : -1.67 (0.18), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 617 TYR 0.017 0.001 TYR A 162 PHE 0.009 0.001 PHE A 407 TRP 0.006 0.001 TRP B 223 HIS 0.003 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00300 (19892) covalent geometry : angle 0.50967 (27016) hydrogen bonds : bond 0.03189 ( 1044) hydrogen bonds : angle 3.02814 ( 3060) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.683 Fit side-chains REVERT: A 141 GLN cc_start: 0.8556 (mm-40) cc_final: 0.7982 (tp-100) REVERT: A 277 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7541 (mpp) REVERT: A 645 MET cc_start: 0.7808 (tpp) cc_final: 0.7562 (tpp) REVERT: B 141 GLN cc_start: 0.8557 (mm-40) cc_final: 0.7932 (tp-100) REVERT: B 277 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7631 (mpp) REVERT: C 141 GLN cc_start: 0.8563 (mm-40) cc_final: 0.7943 (tp-100) REVERT: C 277 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7618 (mpp) REVERT: D 141 GLN cc_start: 0.8549 (mm-40) cc_final: 0.7931 (tp-100) REVERT: D 277 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7621 (mpp) outliers start: 40 outliers final: 28 residues processed: 176 average time/residue: 0.1343 time to fit residues: 37.8977 Evaluate side-chains 188 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 547 PHE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 648 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 119 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 126 optimal weight: 6.9990 chunk 236 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 196 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 100 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.118679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.093745 restraints weight = 35064.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.096161 restraints weight = 23566.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.097793 restraints weight = 18244.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.098936 restraints weight = 15398.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.099525 restraints weight = 13693.195| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 19892 Z= 0.107 Angle : 0.498 8.916 27016 Z= 0.238 Chirality : 0.036 0.123 3092 Planarity : 0.003 0.047 3316 Dihedral : 3.195 12.868 2632 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.61 % Allowed : 15.91 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.17), residues: 2392 helix: 2.32 (0.14), residues: 1436 sheet: 0.11 (0.56), residues: 64 loop : -1.65 (0.18), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 392 TYR 0.016 0.001 TYR A 162 PHE 0.007 0.001 PHE A 407 TRP 0.014 0.001 TRP A 223 HIS 0.002 0.000 HIS C 313 Details of bonding type rmsd covalent geometry : bond 0.00247 (19892) covalent geometry : angle 0.49751 (27016) hydrogen bonds : bond 0.02980 ( 1044) hydrogen bonds : angle 2.90748 ( 3060) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 169 time to evaluate : 0.703 Fit side-chains REVERT: A 141 GLN cc_start: 0.8544 (mm-40) cc_final: 0.7967 (tp-100) REVERT: A 277 MET cc_start: 0.8415 (OUTLIER) cc_final: 0.7846 (mpp) REVERT: A 534 LEU cc_start: 0.4689 (OUTLIER) cc_final: 0.4218 (mt) REVERT: A 607 MET cc_start: 0.8729 (tpt) cc_final: 0.8473 (tpt) REVERT: A 645 MET cc_start: 0.7805 (tpp) cc_final: 0.7473 (tpp) REVERT: A 670 GLU cc_start: 0.7844 (tt0) cc_final: 0.7622 (tp30) REVERT: B 141 GLN cc_start: 0.8544 (mm-40) cc_final: 0.7922 (tp-100) REVERT: B 277 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7503 (mpp) REVERT: B 534 LEU cc_start: 0.4686 (OUTLIER) cc_final: 0.4229 (mt) REVERT: B 607 MET cc_start: 0.8729 (tpt) cc_final: 0.8466 (tpt) REVERT: B 670 GLU cc_start: 0.7867 (tt0) cc_final: 0.7626 (tp30) REVERT: C 141 GLN cc_start: 0.8540 (mm-40) cc_final: 0.7923 (tp-100) REVERT: C 277 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7493 (mpp) REVERT: C 534 LEU cc_start: 0.4672 (OUTLIER) cc_final: 0.4215 (mt) REVERT: D 141 GLN cc_start: 0.8542 (mm-40) cc_final: 0.7919 (tp-100) REVERT: D 277 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7493 (mpp) REVERT: D 534 LEU cc_start: 0.4694 (OUTLIER) cc_final: 0.4219 (mt) outliers start: 54 outliers final: 33 residues processed: 205 average time/residue: 0.1274 time to fit residues: 43.0335 Evaluate side-chains 194 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 153 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 151 LEU Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 547 PHE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 648 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 141 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 188 optimal weight: 0.0570 chunk 167 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 118 optimal weight: 10.0000 chunk 224 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 511 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.118145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.093183 restraints weight = 35196.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.095591 restraints weight = 23747.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.097223 restraints weight = 18426.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.098257 restraints weight = 15572.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.099062 restraints weight = 13908.477| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 19892 Z= 0.116 Angle : 0.520 8.946 27016 Z= 0.245 Chirality : 0.036 0.121 3092 Planarity : 0.003 0.046 3316 Dihedral : 3.189 12.565 2632 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.85 % Allowed : 15.86 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.17), residues: 2392 helix: 2.37 (0.14), residues: 1436 sheet: -0.03 (0.58), residues: 64 loop : -1.67 (0.18), residues: 892 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 100 TYR 0.014 0.001 TYR D 525 PHE 0.008 0.001 PHE B 407 TRP 0.016 0.001 TRP C 223 HIS 0.002 0.001 HIS A 313 Details of bonding type rmsd covalent geometry : bond 0.00273 (19892) covalent geometry : angle 0.52017 (27016) hydrogen bonds : bond 0.03007 ( 1044) hydrogen bonds : angle 2.88920 ( 3060) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 149 time to evaluate : 0.718 Fit side-chains REVERT: A 141 GLN cc_start: 0.8546 (mm-40) cc_final: 0.7937 (tp-100) REVERT: A 277 MET cc_start: 0.8404 (OUTLIER) cc_final: 0.7909 (mpp) REVERT: A 534 LEU cc_start: 0.4860 (OUTLIER) cc_final: 0.4375 (mt) REVERT: A 607 MET cc_start: 0.8766 (tpt) cc_final: 0.8500 (tpt) REVERT: A 645 MET cc_start: 0.7756 (tpp) cc_final: 0.7385 (tpp) REVERT: A 670 GLU cc_start: 0.7889 (tt0) cc_final: 0.7609 (tp30) REVERT: B 141 GLN cc_start: 0.8576 (mm-40) cc_final: 0.7949 (tp-100) REVERT: B 277 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.7884 (mpp) REVERT: B 534 LEU cc_start: 0.4886 (OUTLIER) cc_final: 0.4384 (mt) REVERT: B 607 MET cc_start: 0.8763 (tpt) cc_final: 0.8483 (tpt) REVERT: B 670 GLU cc_start: 0.7890 (tt0) cc_final: 0.7609 (tp30) REVERT: C 141 GLN cc_start: 0.8563 (mm-40) cc_final: 0.7929 (tp-100) REVERT: C 277 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.7878 (mpp) REVERT: C 534 LEU cc_start: 0.4862 (OUTLIER) cc_final: 0.4363 (mt) REVERT: D 141 GLN cc_start: 0.8567 (mm-40) cc_final: 0.7941 (tp-100) REVERT: D 277 MET cc_start: 0.8441 (OUTLIER) cc_final: 0.7883 (mpp) REVERT: D 534 LEU cc_start: 0.4844 (OUTLIER) cc_final: 0.4354 (mt) outliers start: 59 outliers final: 37 residues processed: 191 average time/residue: 0.1135 time to fit residues: 36.4480 Evaluate side-chains 193 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 148 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 308 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 547 PHE Chi-restraints excluded: chain A residue 557 SER Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 308 ILE Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 557 SER Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 308 ILE Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 547 PHE Chi-restraints excluded: chain C residue 557 SER Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 308 ILE Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 557 SER Chi-restraints excluded: chain D residue 648 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 51 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 42 optimal weight: 5.9990 chunk 194 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 chunk 107 optimal weight: 10.0000 chunk 217 optimal weight: 0.0020 chunk 96 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.119672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.094774 restraints weight = 34838.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.097176 restraints weight = 23492.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.098820 restraints weight = 18289.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.099941 restraints weight = 15430.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100686 restraints weight = 13743.574| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 19892 Z= 0.096 Angle : 0.496 8.914 27016 Z= 0.235 Chirality : 0.035 0.121 3092 Planarity : 0.003 0.046 3316 Dihedral : 3.127 12.624 2632 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.13 % Allowed : 16.73 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.47 (0.17), residues: 2392 helix: 2.45 (0.14), residues: 1436 sheet: 0.87 (0.57), residues: 56 loop : -1.60 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 100 TYR 0.015 0.001 TYR D 525 PHE 0.007 0.001 PHE A 551 TRP 0.013 0.001 TRP C 223 HIS 0.002 0.000 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00217 (19892) covalent geometry : angle 0.49578 (27016) hydrogen bonds : bond 0.02782 ( 1044) hydrogen bonds : angle 2.77962 ( 3060) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 0.826 Fit side-chains REVERT: A 141 GLN cc_start: 0.8541 (mm-40) cc_final: 0.7944 (tp-100) REVERT: A 277 MET cc_start: 0.8343 (OUTLIER) cc_final: 0.7817 (mpp) REVERT: A 534 LEU cc_start: 0.4801 (OUTLIER) cc_final: 0.4309 (mt) REVERT: A 607 MET cc_start: 0.8748 (tpt) cc_final: 0.8462 (tpt) REVERT: A 670 GLU cc_start: 0.7864 (tt0) cc_final: 0.7553 (tp30) REVERT: B 141 GLN cc_start: 0.8559 (mm-40) cc_final: 0.7943 (tp-100) REVERT: B 277 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7901 (mpp) REVERT: B 534 LEU cc_start: 0.4820 (OUTLIER) cc_final: 0.4326 (mt) REVERT: B 607 MET cc_start: 0.8742 (tpt) cc_final: 0.8444 (tpt) REVERT: B 670 GLU cc_start: 0.7864 (tt0) cc_final: 0.7556 (tp30) REVERT: C 141 GLN cc_start: 0.8553 (mm-40) cc_final: 0.7933 (tp-100) REVERT: C 277 MET cc_start: 0.8405 (OUTLIER) cc_final: 0.7888 (mpp) REVERT: C 534 LEU cc_start: 0.4795 (OUTLIER) cc_final: 0.4303 (mt) REVERT: C 670 GLU cc_start: 0.7871 (tt0) cc_final: 0.7638 (tp30) REVERT: D 141 GLN cc_start: 0.8551 (mm-40) cc_final: 0.7930 (tp-100) REVERT: D 277 MET cc_start: 0.8408 (OUTLIER) cc_final: 0.7906 (mpp) REVERT: D 534 LEU cc_start: 0.4796 (OUTLIER) cc_final: 0.4296 (mt) REVERT: D 670 GLU cc_start: 0.7870 (tt0) cc_final: 0.7635 (tp30) outliers start: 44 outliers final: 29 residues processed: 182 average time/residue: 0.1214 time to fit residues: 37.0348 Evaluate side-chains 188 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 151 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 287 LEU Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 648 THR Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 537 LEU Chi-restraints excluded: chain B residue 545 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain B residue 547 PHE Chi-restraints excluded: chain B residue 558 LEU Chi-restraints excluded: chain B residue 648 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain C residue 545 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain C residue 547 PHE Chi-restraints excluded: chain C residue 558 LEU Chi-restraints excluded: chain C residue 648 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 537 LEU Chi-restraints excluded: chain D residue 545 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 547 PHE Chi-restraints excluded: chain D residue 648 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 169 optimal weight: 0.0670 chunk 37 optimal weight: 4.9990 chunk 149 optimal weight: 0.1980 chunk 176 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 208 optimal weight: 0.5980 chunk 209 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 77 optimal weight: 0.0980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.122436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.097492 restraints weight = 34922.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.100094 restraints weight = 23044.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.101855 restraints weight = 17582.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.102969 restraints weight = 14663.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.103745 restraints weight = 12991.832| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19892 Z= 0.080 Angle : 0.482 9.185 27016 Z= 0.228 Chirality : 0.035 0.130 3092 Planarity : 0.003 0.045 3316 Dihedral : 2.987 11.131 2632 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.26 % Allowed : 17.65 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.17), residues: 2392 helix: 2.58 (0.14), residues: 1436 sheet: 0.82 (0.55), residues: 56 loop : -1.58 (0.18), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 100 TYR 0.014 0.001 TYR B 525 PHE 0.008 0.001 PHE A 551 TRP 0.012 0.001 TRP C 223 HIS 0.002 0.000 HIS D 651 Details of bonding type rmsd covalent geometry : bond 0.00168 (19892) covalent geometry : angle 0.48152 (27016) hydrogen bonds : bond 0.02421 ( 1044) hydrogen bonds : angle 2.61610 ( 3060) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4784 Ramachandran restraints generated. 2392 Oldfield, 0 Emsley, 2392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 0.611 Fit side-chains REVERT: A 277 MET cc_start: 0.8295 (OUTLIER) cc_final: 0.7888 (mmt) REVERT: A 534 LEU cc_start: 0.4523 (OUTLIER) cc_final: 0.4203 (mt) REVERT: A 670 GLU cc_start: 0.7864 (tt0) cc_final: 0.7413 (tp30) REVERT: B 141 GLN cc_start: 0.8569 (mm-40) cc_final: 0.7959 (tp-100) REVERT: B 277 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.8000 (mmt) REVERT: B 534 LEU cc_start: 0.4539 (OUTLIER) cc_final: 0.4221 (mt) REVERT: B 670 GLU cc_start: 0.7868 (tt0) cc_final: 0.7421 (tp30) REVERT: C 141 GLN cc_start: 0.8569 (mm-40) cc_final: 0.7957 (tp-100) REVERT: C 277 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7963 (mmt) REVERT: C 534 LEU cc_start: 0.4519 (OUTLIER) cc_final: 0.4203 (mt) REVERT: C 670 GLU cc_start: 0.7830 (tt0) cc_final: 0.7430 (tp30) REVERT: D 141 GLN cc_start: 0.8580 (mm-40) cc_final: 0.7984 (tp-100) REVERT: D 277 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.7961 (mmt) REVERT: D 534 LEU cc_start: 0.4361 (OUTLIER) cc_final: 0.4039 (mt) REVERT: D 670 GLU cc_start: 0.7824 (tt0) cc_final: 0.7446 (tp30) outliers start: 26 outliers final: 10 residues processed: 181 average time/residue: 0.1198 time to fit residues: 36.8670 Evaluate side-chains 168 residues out of total 2164 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 150 time to evaluate : 0.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 277 MET Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 107 THR Chi-restraints excluded: chain B residue 277 MET Chi-restraints excluded: chain B residue 534 LEU Chi-restraints excluded: chain B residue 546 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 277 MET Chi-restraints excluded: chain C residue 534 LEU Chi-restraints excluded: chain C residue 546 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 277 MET Chi-restraints excluded: chain D residue 534 LEU Chi-restraints excluded: chain D residue 546 VAL Chi-restraints excluded: chain D residue 558 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 185 optimal weight: 4.9990 chunk 133 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 177 optimal weight: 6.9990 chunk 238 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 136 optimal weight: 6.9990 chunk 90 optimal weight: 0.0170 chunk 131 optimal weight: 4.9990 chunk 122 optimal weight: 20.0000 chunk 179 optimal weight: 10.0000 overall best weight: 3.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.114712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.089705 restraints weight = 35396.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.091959 restraints weight = 24283.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.093375 restraints weight = 19088.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.094416 restraints weight = 16361.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.094844 restraints weight = 14696.074| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 19892 Z= 0.233 Angle : 0.633 8.699 27016 Z= 0.303 Chirality : 0.040 0.135 3092 Planarity : 0.003 0.045 3316 Dihedral : 3.443 13.512 2632 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.60 % Allowed : 17.12 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.17), residues: 2392 helix: 2.17 (0.14), residues: 1444 sheet: -0.27 (0.58), residues: 64 loop : -1.70 (0.17), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 100 TYR 0.014 0.002 TYR C 629 PHE 0.023 0.002 PHE A 330 TRP 0.014 0.001 TRP D 223 HIS 0.003 0.001 HIS D 169 Details of bonding type rmsd covalent geometry : bond 0.00562 (19892) covalent geometry : angle 0.63279 (27016) hydrogen bonds : bond 0.03742 ( 1044) hydrogen bonds : angle 3.25612 ( 3060) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2508.99 seconds wall clock time: 44 minutes 40.26 seconds (2680.26 seconds total)