Starting phenix.real_space_refine on Wed Apr 30 23:23:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iet_35393/04_2025/8iet_35393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iet_35393/04_2025/8iet_35393.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iet_35393/04_2025/8iet_35393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iet_35393/04_2025/8iet_35393.map" model { file = "/net/cci-nas-00/data/ceres_data/8iet_35393/04_2025/8iet_35393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iet_35393/04_2025/8iet_35393.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 38 5.16 5 C 6700 2.51 5 N 1670 2.21 5 O 1776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10184 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5092 Classifications: {'peptide': 653} Link IDs: {'PTRANS': 28, 'TRANS': 624} Chain breaks: 4 Chain: "B" Number of atoms: 5092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 653, 5092 Classifications: {'peptide': 653} Link IDs: {'PTRANS': 28, 'TRANS': 624} Chain breaks: 4 Time building chain proxies: 6.51, per 1000 atoms: 0.64 Number of scatterers: 10184 At special positions: 0 Unit cell: (102.315, 115.239, 103.392, 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 38 16.00 O 1776 8.00 N 1670 7.00 C 6700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.5 seconds 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 8 sheets defined 52.4% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 50 through 58 removed outlier: 4.061A pdb=" N SER A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 62 Processing helix chain 'A' and resid 68 through 73 removed outlier: 3.603A pdb=" N LEU A 73 " --> pdb=" O LEU A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 82 removed outlier: 3.796A pdb=" N VAL A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER A 79 " --> pdb=" O SER A 75 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER A 82 " --> pdb=" O VAL A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 95 Processing helix chain 'A' and resid 101 through 106 Processing helix chain 'A' and resid 110 through 120 removed outlier: 3.542A pdb=" N ILE A 115 " --> pdb=" O PHE A 111 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU A 117 " --> pdb=" O ALA A 113 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE A 118 " --> pdb=" O ILE A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 4.078A pdb=" N SER A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 180 removed outlier: 3.619A pdb=" N ALA A 177 " --> pdb=" O ARG A 173 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA A 178 " --> pdb=" O VAL A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 192 removed outlier: 3.954A pdb=" N GLN A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 3.707A pdb=" N LEU A 205 " --> pdb=" O VAL A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 removed outlier: 4.116A pdb=" N THR A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS A 220 " --> pdb=" O ALA A 216 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 230 removed outlier: 3.831A pdb=" N ILE A 229 " --> pdb=" O GLN A 225 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 225 through 230' Processing helix chain 'A' and resid 242 through 251 removed outlier: 3.538A pdb=" N VAL A 246 " --> pdb=" O SER A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 257 removed outlier: 4.093A pdb=" N THR A 257 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 282 removed outlier: 3.738A pdb=" N SER A 273 " --> pdb=" O LEU A 269 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 304 removed outlier: 4.594A pdb=" N THR A 297 " --> pdb=" O GLU A 293 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 339 removed outlier: 3.564A pdb=" N PHE A 336 " --> pdb=" O ASP A 332 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASN A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 347 removed outlier: 3.521A pdb=" N ALA A 347 " --> pdb=" O CYS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 366 removed outlier: 3.593A pdb=" N ALA A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER A 359 " --> pdb=" O PHE A 355 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR A 361 " --> pdb=" O VAL A 357 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 363 " --> pdb=" O SER A 359 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 364 " --> pdb=" O VAL A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 377 Processing helix chain 'A' and resid 380 through 388 removed outlier: 3.921A pdb=" N GLY A 386 " --> pdb=" O ASN A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 407 removed outlier: 3.523A pdb=" N ALA A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY A 407 " --> pdb=" O GLN A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.592A pdb=" N ALA A 444 " --> pdb=" O LEU A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 456 removed outlier: 3.623A pdb=" N PHE A 455 " --> pdb=" O LEU A 452 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA A 456 " --> pdb=" O MET A 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 452 through 456' Processing helix chain 'A' and resid 457 through 462 removed outlier: 3.518A pdb=" N TRP A 462 " --> pdb=" O ILE A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 469 through 483 removed outlier: 3.512A pdb=" N ILE A 480 " --> pdb=" O PHE A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 496 removed outlier: 3.692A pdb=" N PHE A 494 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 499 No H-bonds generated for 'chain 'A' and resid 497 through 499' Processing helix chain 'A' and resid 548 through 557 Processing helix chain 'A' and resid 565 through 580 removed outlier: 3.546A pdb=" N ARG A 571 " --> pdb=" O ILE A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 616 Processing helix chain 'A' and resid 660 through 676 removed outlier: 3.616A pdb=" N ARG A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY A 666 " --> pdb=" O SER A 662 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER A 669 " --> pdb=" O ARG A 665 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE A 674 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 676 " --> pdb=" O GLN A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 695 removed outlier: 3.739A pdb=" N ILE A 691 " --> pdb=" O ASP A 687 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU A 694 " --> pdb=" O PHE A 690 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A 695 " --> pdb=" O ILE A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 712 through 721 Processing helix chain 'B' and resid 50 through 58 removed outlier: 4.061A pdb=" N SER B 56 " --> pdb=" O ARG B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 62 Processing helix chain 'B' and resid 68 through 73 removed outlier: 3.603A pdb=" N LEU B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 82 removed outlier: 3.796A pdb=" N VAL B 78 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N SER B 79 " --> pdb=" O SER B 75 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N GLY B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER B 82 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 95 Processing helix chain 'B' and resid 101 through 106 Processing helix chain 'B' and resid 110 through 120 removed outlier: 3.542A pdb=" N ILE B 115 " --> pdb=" O PHE B 111 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LEU B 117 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N PHE B 118 " --> pdb=" O ILE B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 146 removed outlier: 4.078A pdb=" N SER B 142 " --> pdb=" O GLY B 138 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER B 146 " --> pdb=" O SER B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 180 removed outlier: 3.619A pdb=" N ALA B 177 " --> pdb=" O ARG B 173 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA B 178 " --> pdb=" O VAL B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 192 removed outlier: 3.954A pdb=" N GLN B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 205 removed outlier: 3.707A pdb=" N LEU B 205 " --> pdb=" O VAL B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 225 removed outlier: 4.116A pdb=" N THR B 215 " --> pdb=" O SER B 211 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N HIS B 220 " --> pdb=" O ALA B 216 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 230 removed outlier: 3.831A pdb=" N ILE B 229 " --> pdb=" O GLN B 225 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 225 through 230' Processing helix chain 'B' and resid 242 through 251 removed outlier: 3.537A pdb=" N VAL B 246 " --> pdb=" O SER B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 257 removed outlier: 4.093A pdb=" N THR B 257 " --> pdb=" O ILE B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 266 through 282 removed outlier: 3.738A pdb=" N SER B 273 " --> pdb=" O LEU B 269 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LYS B 276 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 280 " --> pdb=" O LYS B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 304 removed outlier: 4.594A pdb=" N THR B 297 " --> pdb=" O GLU B 293 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 removed outlier: 3.564A pdb=" N PHE B 336 " --> pdb=" O ASP B 332 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASN B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 339 " --> pdb=" O THR B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 347 removed outlier: 3.521A pdb=" N ALA B 347 " --> pdb=" O CYS B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 366 removed outlier: 3.593A pdb=" N ALA B 358 " --> pdb=" O ALA B 354 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B 359 " --> pdb=" O PHE B 355 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL B 360 " --> pdb=" O SER B 356 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N TYR B 361 " --> pdb=" O VAL B 357 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU B 363 " --> pdb=" O SER B 359 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS B 364 " --> pdb=" O VAL B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 377 Processing helix chain 'B' and resid 380 through 388 removed outlier: 3.921A pdb=" N GLY B 386 " --> pdb=" O ASN B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 407 removed outlier: 3.523A pdb=" N ALA B 401 " --> pdb=" O LEU B 397 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 407 " --> pdb=" O GLN B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 427 Processing helix chain 'B' and resid 439 through 444 removed outlier: 3.592A pdb=" N ALA B 444 " --> pdb=" O LEU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 removed outlier: 3.623A pdb=" N PHE B 455 " --> pdb=" O LEU B 452 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA B 456 " --> pdb=" O MET B 453 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 452 through 456' Processing helix chain 'B' and resid 457 through 462 removed outlier: 3.518A pdb=" N TRP B 462 " --> pdb=" O ILE B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 removed outlier: 3.512A pdb=" N ILE B 480 " --> pdb=" O PHE B 476 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 496 removed outlier: 3.692A pdb=" N PHE B 494 " --> pdb=" O ALA B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 497 through 499 No H-bonds generated for 'chain 'B' and resid 497 through 499' Processing helix chain 'B' and resid 548 through 557 Processing helix chain 'B' and resid 565 through 580 removed outlier: 3.546A pdb=" N ARG B 571 " --> pdb=" O ILE B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 616 Processing helix chain 'B' and resid 660 through 676 removed outlier: 3.616A pdb=" N ARG B 665 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLY B 666 " --> pdb=" O SER B 662 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 669 " --> pdb=" O ARG B 665 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 674 " --> pdb=" O ILE B 670 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG B 676 " --> pdb=" O GLN B 672 " (cutoff:3.500A) Processing helix chain 'B' and resid 687 through 695 removed outlier: 3.739A pdb=" N ILE B 691 " --> pdb=" O ASP B 687 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU B 694 " --> pdb=" O PHE B 690 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN B 695 " --> pdb=" O ILE B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 712 through 721 Processing sheet with id=AA1, first strand: chain 'A' and resid 520 through 522 Processing sheet with id=AA2, first strand: chain 'A' and resid 520 through 522 removed outlier: 3.909A pdb=" N ARG A 539 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N PHE A 538 " --> pdb=" O ASP A 652 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 648 through 649 Processing sheet with id=AA4, first strand: chain 'A' and resid 683 through 684 removed outlier: 6.736A pdb=" N ILE A 683 " --> pdb=" O PHE A 710 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 520 through 522 Processing sheet with id=AA6, first strand: chain 'B' and resid 520 through 522 removed outlier: 3.909A pdb=" N ARG B 539 " --> pdb=" O SER B 509 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N PHE B 538 " --> pdb=" O ASP B 652 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 648 through 649 Processing sheet with id=AA8, first strand: chain 'B' and resid 683 through 684 removed outlier: 6.736A pdb=" N ILE B 683 " --> pdb=" O PHE B 710 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 312 hydrogen bonds defined for protein. 876 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: 3.25 Time building geometry restraints manager: 2.89 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: 3146 1.34 - 1.46: 2041 1.46 - 1.58: 5157 1.58 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 10402 Sorted by residual: bond pdb=" C ASP B 239 " pdb=" N PRO B 240 " ideal model delta sigma weight residual 1.331 1.394 -0.063 1.21e-02 6.83e+03 2.72e+01 bond pdb=" C ASP A 239 " pdb=" N PRO A 240 " ideal model delta sigma weight residual 1.331 1.394 -0.063 1.21e-02 6.83e+03 2.68e+01 bond pdb=" N PRO A 240 " pdb=" CD PRO A 240 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.56e+01 bond pdb=" N PRO B 240 " pdb=" CD PRO B 240 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.51e+01 bond pdb=" CA ASP B 239 " pdb=" C ASP B 239 " ideal model delta sigma weight residual 1.524 1.545 -0.021 1.26e-02 6.30e+03 2.88e+00 ... (remaining 10397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 13872 2.78 - 5.56: 226 5.56 - 8.34: 6 8.34 - 11.12: 6 11.12 - 13.90: 2 Bond angle restraints: 14112 Sorted by residual: angle pdb=" N THR A 238 " pdb=" CA THR A 238 " pdb=" C THR A 238 " ideal model delta sigma weight residual 110.80 121.50 -10.70 2.13e+00 2.20e-01 2.52e+01 angle pdb=" N THR B 238 " pdb=" CA THR B 238 " pdb=" C THR B 238 " ideal model delta sigma weight residual 110.80 121.31 -10.51 2.13e+00 2.20e-01 2.44e+01 angle pdb=" C ASP B 239 " pdb=" N PRO B 240 " pdb=" CA PRO B 240 " ideal model delta sigma weight residual 120.11 114.59 5.52 1.12e+00 7.97e-01 2.43e+01 angle pdb=" C ASP A 239 " pdb=" N PRO A 240 " pdb=" CA PRO A 240 " ideal model delta sigma weight residual 120.11 114.60 5.51 1.12e+00 7.97e-01 2.42e+01 angle pdb=" C SER A 17 " pdb=" N THR A 18 " pdb=" CA THR A 18 " ideal model delta sigma weight residual 121.54 130.88 -9.34 1.91e+00 2.74e-01 2.39e+01 ... (remaining 14107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 5425 16.29 - 32.58: 627 32.58 - 48.87: 105 48.87 - 65.16: 15 65.16 - 81.45: 4 Dihedral angle restraints: 6176 sinusoidal: 2400 harmonic: 3776 Sorted by residual: dihedral pdb=" CA LEU A 435 " pdb=" C LEU A 435 " pdb=" N GLN A 436 " pdb=" CA GLN A 436 " ideal model delta harmonic sigma weight residual -180.00 -152.67 -27.33 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA LEU B 435 " pdb=" C LEU B 435 " pdb=" N GLN B 436 " pdb=" CA GLN B 436 " ideal model delta harmonic sigma weight residual -180.00 -152.67 -27.33 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA SER A 438 " pdb=" C SER A 438 " pdb=" N VAL A 439 " pdb=" CA VAL A 439 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 6173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1489 0.079 - 0.157: 185 0.157 - 0.236: 4 0.236 - 0.315: 0 0.315 - 0.393: 4 Chirality restraints: 1682 Sorted by residual: chirality pdb=" CA ASP B 239 " pdb=" N ASP B 239 " pdb=" C ASP B 239 " pdb=" CB ASP B 239 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CA ASP A 239 " pdb=" N ASP A 239 " pdb=" C ASP A 239 " pdb=" CB ASP A 239 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA THR B 238 " pdb=" N THR B 238 " pdb=" C THR B 238 " pdb=" CB THR B 238 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 1679 not shown) Planarity restraints: 1750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 100 " 0.049 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO B 101 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 101 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 101 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 100 " 0.049 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO A 101 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 433 " 0.039 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO A 434 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 434 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 434 " 0.032 5.00e-02 4.00e+02 ... (remaining 1747 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1250 2.75 - 3.28: 9001 3.28 - 3.82: 15215 3.82 - 4.36: 19244 4.36 - 4.90: 33420 Nonbonded interactions: 78130 Sorted by model distance: nonbonded pdb=" O THR A 238 " pdb=" O ASP A 239 " model vdw 2.207 3.040 nonbonded pdb=" O THR B 238 " pdb=" O ASP B 239 " model vdw 2.277 3.040 nonbonded pdb=" O GLY B 487 " pdb=" OG SER B 491 " model vdw 2.337 3.040 nonbonded pdb=" O GLY A 487 " pdb=" OG SER A 491 " model vdw 2.337 3.040 nonbonded pdb=" OD1 ASP A 465 " pdb=" OH TYR B 697 " model vdw 2.339 3.040 ... (remaining 78125 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.570 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: 0.460 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 27.620 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.070 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:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 : 0.006 0.063 10402 Z= 0.271 Angle : 0.879 13.898 14112 Z= 0.493 Chirality : 0.055 0.393 1682 Planarity : 0.007 0.073 1750 Dihedral : 13.904 81.452 3736 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.91 % Favored : 93.86 % Rotamer: Outliers : 0.45 % Allowed : 8.41 % Favored : 91.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.60 (0.14), residues: 1286 helix: -5.02 (0.05), residues: 734 sheet: -1.99 (0.87), residues: 36 loop : -3.26 (0.21), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 472 HIS 0.003 0.001 HIS A 220 PHE 0.022 0.002 PHE A 130 TYR 0.022 0.002 TYR A 9 ARG 0.002 0.000 ARG B 539 Details of bonding type rmsd hydrogen bonds : bond 0.32578 ( 308) hydrogen bonds : angle 11.44325 ( 876) covalent geometry : bond 0.00604 (10402) covalent geometry : angle 0.87923 (14112) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 168 time to evaluate : 1.079 Fit side-chains REVERT: A 48 GLN cc_start: 0.6837 (mm-40) cc_final: 0.6605 (tp-100) REVERT: A 55 LEU cc_start: 0.8359 (mp) cc_final: 0.7939 (tt) REVERT: A 293 GLU cc_start: 0.7550 (mt-10) cc_final: 0.6512 (tt0) REVERT: A 363 LEU cc_start: 0.8131 (mp) cc_final: 0.7868 (mp) REVERT: A 612 GLN cc_start: 0.7483 (mt0) cc_final: 0.6736 (mt0) REVERT: B 48 GLN cc_start: 0.6852 (mm-40) cc_final: 0.6618 (tp-100) REVERT: B 55 LEU cc_start: 0.8357 (mp) cc_final: 0.7939 (tt) REVERT: B 293 GLU cc_start: 0.7548 (mt-10) cc_final: 0.6511 (tt0) REVERT: B 363 LEU cc_start: 0.8121 (mp) cc_final: 0.7862 (mp) REVERT: B 612 GLN cc_start: 0.7490 (mt0) cc_final: 0.6743 (mt0) outliers start: 5 outliers final: 3 residues processed: 171 average time/residue: 0.2376 time to fit residues: 56.2410 Evaluate side-chains 113 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 320 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 0.1980 chunk 98 optimal weight: 4.9990 chunk 54 optimal weight: 20.0000 chunk 33 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 2.9990 chunk 39 optimal weight: 0.0470 chunk 61 optimal weight: 0.8980 chunk 75 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 overall best weight: 0.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 447 ASN A 454 GLN A 495 GLN A 504 GLN B 8 GLN B 447 ASN B 454 GLN B 495 GLN B 504 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.139860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.117267 restraints weight = 11823.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.116172 restraints weight = 14295.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.117020 restraints weight = 11992.938| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10402 Z= 0.112 Angle : 0.564 7.610 14112 Z= 0.303 Chirality : 0.043 0.177 1682 Planarity : 0.005 0.051 1750 Dihedral : 6.102 58.740 1395 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 1.70 % Allowed : 12.70 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.07 (0.17), residues: 1286 helix: -3.71 (0.12), residues: 746 sheet: -2.02 (0.88), residues: 34 loop : -2.62 (0.23), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.006 0.001 HIS B 237 PHE 0.022 0.001 PHE B 562 TYR 0.013 0.001 TYR B 9 ARG 0.003 0.000 ARG A 502 Details of bonding type rmsd hydrogen bonds : bond 0.04722 ( 308) hydrogen bonds : angle 5.71757 ( 876) covalent geometry : bond 0.00237 (10402) covalent geometry : angle 0.56421 (14112) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 133 time to evaluate : 1.205 Fit side-chains REVERT: A 55 LEU cc_start: 0.8315 (mp) cc_final: 0.7858 (tt) REVERT: A 293 GLU cc_start: 0.7182 (mt-10) cc_final: 0.6132 (tt0) REVERT: A 363 LEU cc_start: 0.8166 (mp) cc_final: 0.7808 (mp) REVERT: A 612 GLN cc_start: 0.7538 (mt0) cc_final: 0.6772 (mt0) REVERT: B 55 LEU cc_start: 0.8314 (mp) cc_final: 0.7861 (tt) REVERT: B 293 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6134 (tt0) REVERT: B 363 LEU cc_start: 0.8170 (mp) cc_final: 0.7811 (mp) REVERT: B 612 GLN cc_start: 0.7537 (mt0) cc_final: 0.6770 (mt0) outliers start: 19 outliers final: 9 residues processed: 141 average time/residue: 0.1765 time to fit residues: 38.5797 Evaluate side-chains 124 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 115 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 337 GLN Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 337 GLN Chi-restraints excluded: chain B residue 712 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 39 optimal weight: 0.0470 chunk 1 optimal weight: 0.0020 chunk 101 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 92 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 overall best weight: 0.5286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.142243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.118697 restraints weight = 11817.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.117902 restraints weight = 14706.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.119101 restraints weight = 13997.873| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10402 Z= 0.091 Angle : 0.492 5.766 14112 Z= 0.263 Chirality : 0.041 0.133 1682 Planarity : 0.004 0.039 1750 Dihedral : 5.329 55.243 1391 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.34 % Allowed : 16.10 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.89 (0.20), residues: 1286 helix: -2.76 (0.16), residues: 756 sheet: -0.91 (1.00), residues: 36 loop : -2.12 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 63 HIS 0.008 0.001 HIS B 237 PHE 0.015 0.001 PHE B 562 TYR 0.009 0.001 TYR B 9 ARG 0.002 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03006 ( 308) hydrogen bonds : angle 4.75452 ( 876) covalent geometry : bond 0.00198 (10402) covalent geometry : angle 0.49177 (14112) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 1.064 Fit side-chains REVERT: A 69 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8259 (mp) REVERT: A 280 GLN cc_start: 0.7164 (OUTLIER) cc_final: 0.5514 (mp10) REVERT: A 363 LEU cc_start: 0.8156 (mp) cc_final: 0.7844 (mt) REVERT: A 410 THR cc_start: 0.8917 (p) cc_final: 0.8702 (t) REVERT: A 554 ARG cc_start: 0.7969 (ttm170) cc_final: 0.7605 (mtm110) REVERT: A 612 GLN cc_start: 0.7470 (mt0) cc_final: 0.6763 (mt0) REVERT: A 715 ASP cc_start: 0.7762 (t0) cc_final: 0.7457 (t0) REVERT: B 69 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8260 (mp) REVERT: B 280 GLN cc_start: 0.7162 (OUTLIER) cc_final: 0.5514 (mp10) REVERT: B 363 LEU cc_start: 0.8155 (mp) cc_final: 0.7841 (mt) REVERT: B 410 THR cc_start: 0.8916 (p) cc_final: 0.8702 (t) REVERT: B 554 ARG cc_start: 0.7971 (ttm170) cc_final: 0.7606 (mtm110) REVERT: B 612 GLN cc_start: 0.7479 (mt0) cc_final: 0.6773 (mt0) REVERT: B 715 ASP cc_start: 0.7779 (t0) cc_final: 0.7473 (t0) outliers start: 15 outliers final: 7 residues processed: 127 average time/residue: 0.1932 time to fit residues: 36.4557 Evaluate side-chains 129 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 118 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 712 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 73 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 20 optimal weight: 3.9990 chunk 26 optimal weight: 0.0010 chunk 103 optimal weight: 0.3980 chunk 36 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN B 454 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.142075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.118056 restraints weight = 11717.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.117195 restraints weight = 14904.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.118834 restraints weight = 15680.245| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10402 Z= 0.094 Angle : 0.477 5.174 14112 Z= 0.253 Chirality : 0.041 0.129 1682 Planarity : 0.003 0.033 1750 Dihedral : 5.026 47.383 1391 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.88 % Allowed : 16.28 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.21), residues: 1286 helix: -2.31 (0.17), residues: 766 sheet: -0.72 (1.03), residues: 36 loop : -1.86 (0.26), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 63 HIS 0.003 0.001 HIS B 237 PHE 0.015 0.001 PHE A 130 TYR 0.015 0.001 TYR B 545 ARG 0.002 0.000 ARG A 569 Details of bonding type rmsd hydrogen bonds : bond 0.02720 ( 308) hydrogen bonds : angle 4.40512 ( 876) covalent geometry : bond 0.00218 (10402) covalent geometry : angle 0.47725 (14112) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 1.069 Fit side-chains REVERT: A 69 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8300 (mp) REVERT: A 280 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.5377 (mp10) REVERT: A 363 LEU cc_start: 0.8302 (mp) cc_final: 0.7979 (mt) REVERT: A 410 THR cc_start: 0.8942 (p) cc_final: 0.8736 (t) REVERT: A 554 ARG cc_start: 0.7930 (ttm170) cc_final: 0.7588 (mtm110) REVERT: A 715 ASP cc_start: 0.7746 (t0) cc_final: 0.7387 (t0) REVERT: B 69 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8303 (mp) REVERT: B 280 GLN cc_start: 0.6990 (OUTLIER) cc_final: 0.5477 (mp10) REVERT: B 363 LEU cc_start: 0.8298 (mp) cc_final: 0.7980 (mt) REVERT: B 410 THR cc_start: 0.8937 (p) cc_final: 0.8732 (t) REVERT: B 554 ARG cc_start: 0.7931 (ttm170) cc_final: 0.7591 (mtm110) REVERT: B 715 ASP cc_start: 0.7739 (t0) cc_final: 0.7377 (t0) outliers start: 21 outliers final: 11 residues processed: 140 average time/residue: 0.2003 time to fit residues: 41.8097 Evaluate side-chains 132 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 1.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 712 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 9.9990 chunk 16 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 75 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 107 optimal weight: 5.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.135167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.111243 restraints weight = 11974.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.110116 restraints weight = 16219.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.111634 restraints weight = 16825.025| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.1962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 10402 Z= 0.315 Angle : 0.687 7.730 14112 Z= 0.352 Chirality : 0.049 0.153 1682 Planarity : 0.005 0.037 1750 Dihedral : 5.737 46.219 1391 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.29 % Favored : 94.56 % Rotamer: Outliers : 3.85 % Allowed : 16.46 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.68 (0.21), residues: 1286 helix: -2.48 (0.16), residues: 756 sheet: -1.97 (0.88), residues: 36 loop : -2.15 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 472 HIS 0.005 0.001 HIS A 220 PHE 0.024 0.002 PHE B 130 TYR 0.038 0.003 TYR B 9 ARG 0.002 0.000 ARG B 123 Details of bonding type rmsd hydrogen bonds : bond 0.04332 ( 308) hydrogen bonds : angle 4.81214 ( 876) covalent geometry : bond 0.00790 (10402) covalent geometry : angle 0.68729 (14112) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 115 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.7323 (OUTLIER) cc_final: 0.5800 (mp10) REVERT: A 293 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6289 (tt0) REVERT: A 363 LEU cc_start: 0.8360 (mp) cc_final: 0.8006 (mt) REVERT: A 404 GLU cc_start: 0.6784 (tt0) cc_final: 0.6547 (tt0) REVERT: A 608 LEU cc_start: 0.6719 (OUTLIER) cc_final: 0.6424 (pp) REVERT: A 612 GLN cc_start: 0.7397 (mt0) cc_final: 0.6625 (mt0) REVERT: B 280 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.5885 (mp10) REVERT: B 293 GLU cc_start: 0.7354 (mt-10) cc_final: 0.6293 (tt0) REVERT: B 363 LEU cc_start: 0.8359 (mp) cc_final: 0.8007 (mt) REVERT: B 404 GLU cc_start: 0.6776 (tt0) cc_final: 0.6539 (tt0) REVERT: B 608 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6424 (pp) REVERT: B 612 GLN cc_start: 0.7407 (mt0) cc_final: 0.6630 (mt0) outliers start: 43 outliers final: 27 residues processed: 136 average time/residue: 0.2262 time to fit residues: 45.7105 Evaluate side-chains 138 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 608 LEU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 608 LEU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 712 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 107 optimal weight: 0.6980 chunk 124 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 46 optimal weight: 0.0000 chunk 110 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.140325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.116564 restraints weight = 11818.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.115394 restraints weight = 13286.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.116503 restraints weight = 10636.271| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10402 Z= 0.092 Angle : 0.480 5.115 14112 Z= 0.257 Chirality : 0.041 0.128 1682 Planarity : 0.003 0.036 1750 Dihedral : 5.095 37.493 1391 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.42 % Favored : 96.42 % Rotamer: Outliers : 2.33 % Allowed : 17.98 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.22), residues: 1286 helix: -1.99 (0.18), residues: 748 sheet: -1.34 (0.95), residues: 36 loop : -1.73 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.003 0.000 HIS B 237 PHE 0.011 0.001 PHE A 562 TYR 0.013 0.001 TYR B 545 ARG 0.002 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.02551 ( 308) hydrogen bonds : angle 4.33362 ( 876) covalent geometry : bond 0.00208 (10402) covalent geometry : angle 0.48001 (14112) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.6803 (ptp90) cc_final: 0.6512 (ttp80) REVERT: A 280 GLN cc_start: 0.7243 (OUTLIER) cc_final: 0.5846 (mp10) REVERT: A 363 LEU cc_start: 0.8310 (mp) cc_final: 0.7955 (mt) REVERT: A 404 GLU cc_start: 0.6402 (tt0) cc_final: 0.6160 (tt0) REVERT: A 612 GLN cc_start: 0.7399 (mt0) cc_final: 0.6710 (mt0) REVERT: B 52 ARG cc_start: 0.6812 (ptp90) cc_final: 0.6520 (ttp80) REVERT: B 236 SER cc_start: 0.8440 (OUTLIER) cc_final: 0.8135 (m) REVERT: B 280 GLN cc_start: 0.7236 (OUTLIER) cc_final: 0.5844 (mp10) REVERT: B 363 LEU cc_start: 0.8304 (mp) cc_final: 0.7949 (mt) REVERT: B 404 GLU cc_start: 0.6401 (tt0) cc_final: 0.6157 (tt0) REVERT: B 612 GLN cc_start: 0.7400 (mt0) cc_final: 0.6715 (mt0) outliers start: 26 outliers final: 19 residues processed: 135 average time/residue: 0.1770 time to fit residues: 36.7251 Evaluate side-chains 133 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 640 GLU Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 712 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 58 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 41 optimal weight: 0.9980 chunk 82 optimal weight: 0.4980 chunk 74 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 95 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN B 48 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.141337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.118560 restraints weight = 11843.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.117619 restraints weight = 17623.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.118832 restraints weight = 17415.576| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10402 Z= 0.094 Angle : 0.468 5.080 14112 Z= 0.249 Chirality : 0.041 0.129 1682 Planarity : 0.003 0.035 1750 Dihedral : 4.741 19.515 1391 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.68 % Allowed : 18.52 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.22), residues: 1286 helix: -1.68 (0.19), residues: 734 sheet: -0.91 (1.01), residues: 36 loop : -1.54 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 63 HIS 0.002 0.001 HIS B 237 PHE 0.012 0.001 PHE A 130 TYR 0.012 0.001 TYR B 9 ARG 0.001 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.02410 ( 308) hydrogen bonds : angle 4.15093 ( 876) covalent geometry : bond 0.00220 (10402) covalent geometry : angle 0.46767 (14112) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 117 time to evaluate : 1.564 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.6789 (ptp90) cc_final: 0.6459 (ttp80) REVERT: A 280 GLN cc_start: 0.7203 (OUTLIER) cc_final: 0.5517 (mp10) REVERT: A 363 LEU cc_start: 0.8294 (mp) cc_final: 0.7933 (mt) REVERT: A 612 GLN cc_start: 0.7502 (mt0) cc_final: 0.6841 (mt0) REVERT: B 52 ARG cc_start: 0.6795 (ptp90) cc_final: 0.6464 (ttp80) REVERT: B 280 GLN cc_start: 0.7207 (OUTLIER) cc_final: 0.5521 (mp10) REVERT: B 363 LEU cc_start: 0.8289 (mp) cc_final: 0.7927 (mt) REVERT: B 404 GLU cc_start: 0.6263 (tt0) cc_final: 0.6036 (tt0) REVERT: B 612 GLN cc_start: 0.7504 (mt0) cc_final: 0.6844 (mt0) outliers start: 30 outliers final: 28 residues processed: 138 average time/residue: 0.2046 time to fit residues: 44.4123 Evaluate side-chains 145 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 1.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 640 GLU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 712 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 57 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3423 r_free = 0.3423 target = 0.139831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.114858 restraints weight = 11839.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.114633 restraints weight = 13076.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.115786 restraints weight = 12621.157| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10402 Z= 0.123 Angle : 0.488 5.058 14112 Z= 0.258 Chirality : 0.042 0.126 1682 Planarity : 0.003 0.036 1750 Dihedral : 4.749 21.199 1390 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.58 % Allowed : 17.98 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.22), residues: 1286 helix: -1.61 (0.19), residues: 738 sheet: -1.02 (1.00), residues: 36 loop : -1.47 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.002 0.001 HIS B 220 PHE 0.014 0.001 PHE B 130 TYR 0.016 0.001 TYR B 9 ARG 0.001 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.02682 ( 308) hydrogen bonds : angle 4.17698 ( 876) covalent geometry : bond 0.00303 (10402) covalent geometry : angle 0.48825 (14112) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 124 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.6753 (ptp90) cc_final: 0.6460 (ttp80) REVERT: A 280 GLN cc_start: 0.7179 (OUTLIER) cc_final: 0.5718 (mp10) REVERT: A 363 LEU cc_start: 0.8279 (mp) cc_final: 0.7935 (mt) REVERT: A 404 GLU cc_start: 0.6198 (tt0) cc_final: 0.5996 (tt0) REVERT: A 612 GLN cc_start: 0.7392 (mt0) cc_final: 0.6716 (mt0) REVERT: B 52 ARG cc_start: 0.6760 (ptp90) cc_final: 0.6463 (ttp80) REVERT: B 280 GLN cc_start: 0.7168 (OUTLIER) cc_final: 0.5717 (mp10) REVERT: B 363 LEU cc_start: 0.8249 (mp) cc_final: 0.7881 (mt) REVERT: B 404 GLU cc_start: 0.6251 (tt0) cc_final: 0.6026 (tt0) REVERT: B 612 GLN cc_start: 0.7372 (mt0) cc_final: 0.6713 (mt0) outliers start: 40 outliers final: 32 residues processed: 154 average time/residue: 0.2353 time to fit residues: 54.9446 Evaluate side-chains 152 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 118 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 640 GLU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 712 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 59 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3405 r_free = 0.3405 target = 0.138165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.112907 restraints weight = 11935.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.112783 restraints weight = 12462.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.114400 restraints weight = 12412.900| |-----------------------------------------------------------------------------| r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10402 Z= 0.171 Angle : 0.537 5.063 14112 Z= 0.282 Chirality : 0.044 0.131 1682 Planarity : 0.004 0.036 1750 Dihedral : 4.962 22.079 1390 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.67 % Allowed : 17.26 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.22), residues: 1286 helix: -1.67 (0.18), residues: 746 sheet: -1.50 (0.93), residues: 36 loop : -1.57 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 63 HIS 0.003 0.001 HIS B 220 PHE 0.018 0.001 PHE B 313 TYR 0.022 0.002 TYR A 9 ARG 0.001 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03105 ( 308) hydrogen bonds : angle 4.36671 ( 876) covalent geometry : bond 0.00429 (10402) covalent geometry : angle 0.53704 (14112) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 111 time to evaluate : 1.208 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.6830 (ptp90) cc_final: 0.6528 (ttp80) REVERT: A 280 GLN cc_start: 0.7238 (OUTLIER) cc_final: 0.5764 (mp10) REVERT: A 363 LEU cc_start: 0.8290 (mp) cc_final: 0.7888 (mt) REVERT: A 612 GLN cc_start: 0.7365 (mt0) cc_final: 0.6700 (mt0) REVERT: B 52 ARG cc_start: 0.6841 (ptp90) cc_final: 0.6533 (ttp80) REVERT: B 280 GLN cc_start: 0.7248 (OUTLIER) cc_final: 0.5763 (mp10) REVERT: B 363 LEU cc_start: 0.8299 (mp) cc_final: 0.7891 (mt) REVERT: B 404 GLU cc_start: 0.6339 (tt0) cc_final: 0.6103 (tt0) REVERT: B 612 GLN cc_start: 0.7350 (mt0) cc_final: 0.6697 (mt0) outliers start: 41 outliers final: 35 residues processed: 137 average time/residue: 0.1873 time to fit residues: 38.5482 Evaluate side-chains 143 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 106 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 366 ASP Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 640 GLU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 712 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 88 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 87 optimal weight: 0.2980 chunk 5 optimal weight: 7.9990 chunk 113 optimal weight: 0.6980 chunk 75 optimal weight: 0.6980 chunk 56 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 21 optimal weight: 0.1980 chunk 125 optimal weight: 0.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3446 r_free = 0.3446 target = 0.142053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.117895 restraints weight = 11754.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.117218 restraints weight = 12602.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.118617 restraints weight = 11791.981| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10402 Z= 0.087 Angle : 0.460 5.166 14112 Z= 0.246 Chirality : 0.041 0.132 1682 Planarity : 0.003 0.038 1750 Dihedral : 4.573 21.621 1390 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.59 % Allowed : 18.52 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.23), residues: 1286 helix: -1.37 (0.19), residues: 740 sheet: -1.02 (1.00), residues: 36 loop : -1.39 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 63 HIS 0.002 0.001 HIS A 647 PHE 0.015 0.001 PHE A 313 TYR 0.009 0.001 TYR B 104 ARG 0.001 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.02291 ( 308) hydrogen bonds : angle 4.09599 ( 876) covalent geometry : bond 0.00201 (10402) covalent geometry : angle 0.46019 (14112) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2572 Ramachandran restraints generated. 1286 Oldfield, 0 Emsley, 1286 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.6776 (ptp90) cc_final: 0.6476 (ttp80) REVERT: A 280 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.5500 (mp10) REVERT: A 363 LEU cc_start: 0.8211 (mp) cc_final: 0.7870 (mt) REVERT: A 612 GLN cc_start: 0.7423 (mt0) cc_final: 0.6754 (mt0) REVERT: B 52 ARG cc_start: 0.6789 (ptp90) cc_final: 0.6484 (ttp80) REVERT: B 280 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.5482 (mp10) REVERT: B 363 LEU cc_start: 0.8207 (mp) cc_final: 0.7802 (mt) REVERT: B 612 GLN cc_start: 0.7404 (mt0) cc_final: 0.6744 (mt0) outliers start: 29 outliers final: 27 residues processed: 135 average time/residue: 0.2000 time to fit residues: 40.4034 Evaluate side-chains 141 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 1.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 661 VAL Chi-restraints excluded: chain A residue 673 GLU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 320 ASP Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 640 GLU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 712 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 124 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 90 optimal weight: 0.4980 chunk 123 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 overall best weight: 1.0988 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.141020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.116661 restraints weight = 11758.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.115445 restraints weight = 17703.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.117153 restraints weight = 16825.195| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10402 Z= 0.108 Angle : 0.473 5.130 14112 Z= 0.250 Chirality : 0.041 0.128 1682 Planarity : 0.003 0.037 1750 Dihedral : 4.563 21.012 1390 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.95 % Allowed : 18.25 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.23), residues: 1286 helix: -1.31 (0.19), residues: 752 sheet: -0.96 (1.01), residues: 36 loop : -1.45 (0.26), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 63 HIS 0.002 0.001 HIS A 220 PHE 0.016 0.001 PHE A 313 TYR 0.027 0.001 TYR A 361 ARG 0.001 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.02474 ( 308) hydrogen bonds : angle 4.11042 ( 876) covalent geometry : bond 0.00266 (10402) covalent geometry : angle 0.47275 (14112) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3233.39 seconds wall clock time: 58 minutes 26.33 seconds (3506.33 seconds total)