Starting phenix.real_space_refine on Fri Feb 14 08:51:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iet_35393/02_2025/8iet_35393.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iet_35393/02_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_35393/02_2025/8iet_35393.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iet_35393/02_2025/8iet_35393.map" model { file = "/net/cci-nas-00/data/ceres_data/8iet_35393/02_2025/8iet_35393.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iet_35393/02_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 6.04, per 1000 atoms: 0.59 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: 2.36 Conformation dependent library (CDL) restraints added in 1.2 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: 1.29 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: 2.99 Time building geometry restraints manager: 2.76 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: 0.05 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: 0.530 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.900 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.810 ------------------------------------------------------------------------------- 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= 0.389 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 *********************** 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 : 1.129 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: 0.2461 time to fit residues: 58.4120 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 : 1.084 ------------------------------------------------------------------------------- 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 = 0.117271 restraints weight = 11823.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.116168 restraints weight = 14291.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.117014 restraints weight = 11992.686| |-----------------------------------------------------------------------------| 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= 0.154 Angle : 0.564 7.611 14112 Z= 0.303 Chirality : 0.043 0.177 1682 Planarity : 0.005 0.051 1750 Dihedral : 6.102 58.742 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 *********************** 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 : 1.063 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: 0.6771 (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: 0.6133 (tt0) REVERT: B 363 LEU cc_start: 0.8170 (mp) cc_final: 0.7811 (mp) REVERT: B 612 GLN cc_start: 0.7536 (mt0) cc_final: 0.6770 (mt0) outliers start: 19 outliers final: 9 residues processed: 141 average time/residue: 0.1725 time to fit residues: 37.1863 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 : 1.073 ------------------------------------------------------------------------------- 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: 0.9990 chunk 85 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 1 optimal weight: 0.0170 chunk 101 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.141933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.117924 restraints weight = 11832.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.116938 restraints weight = 14820.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.119368 restraints weight = 14169.529| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1690 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= 0.132 Angle : 0.494 5.787 14112 Z= 0.264 Chirality : 0.041 0.132 1682 Planarity : 0.004 0.039 1750 Dihedral : 5.326 55.015 1391 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.43 % Allowed : 16.01 % 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: -3.90 (0.20), residues: 1286 helix: -2.77 (0.16), residues: 756 sheet: -0.95 (0.99), 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 0.010 0.001 HIS B 237 PHE 0.016 0.001 PHE B 562 TYR 0.010 0.001 TYR A 9 ARG 0.002 0.000 ARG B 52 *********************** 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 136 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8250 (mp) REVERT: A 280 GLN cc_start: 0.7126 (OUTLIER) cc_final: 0.5484 (mp10) REVERT: A 363 LEU cc_start: 0.8215 (mp) cc_final: 0.7894 (mt) REVERT: A 410 THR cc_start: 0.8933 (p) cc_final: 0.8719 (t) REVERT: A 554 ARG cc_start: 0.7945 (ttm170) cc_final: 0.7568 (mtm110) REVERT: A 612 GLN cc_start: 0.7436 (mt0) cc_final: 0.6736 (mt0) REVERT: A 715 ASP cc_start: 0.7773 (t0) cc_final: 0.7469 (t0) REVERT: B 69 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8248 (mp) REVERT: B 280 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.5470 (mp10) REVERT: B 363 LEU cc_start: 0.8214 (mp) cc_final: 0.7895 (mt) REVERT: B 410 THR cc_start: 0.8931 (p) cc_final: 0.8715 (t) REVERT: B 554 ARG cc_start: 0.7941 (ttm170) cc_final: 0.7566 (mtm110) REVERT: B 612 GLN cc_start: 0.7447 (mt0) cc_final: 0.6746 (mt0) REVERT: B 715 ASP cc_start: 0.7776 (t0) cc_final: 0.7467 (t0) outliers start: 16 outliers final: 8 residues processed: 127 average time/residue: 0.1992 time to fit residues: 37.3437 Evaluate side-chains 128 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.147 ------------------------------------------------------------------------------- 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 451 MET 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: 0.5980 chunk 45 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 0.0770 chunk 103 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 454 GLN B 48 GLN B 454 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.141782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.117501 restraints weight = 11703.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.116337 restraints weight = 16246.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.117974 restraints weight = 15920.768| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10402 Z= 0.149 Angle : 0.476 5.176 14112 Z= 0.253 Chirality : 0.041 0.130 1682 Planarity : 0.003 0.033 1750 Dihedral : 5.007 46.213 1391 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.61 % Allowed : 16.64 % Favored : 81.75 % 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: -3.32 (0.21), residues: 1286 helix: -2.31 (0.17), residues: 758 sheet: -0.78 (1.02), residues: 36 loop : -1.84 (0.26), residues: 492 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 B 130 TYR 0.015 0.001 TYR B 545 ARG 0.002 0.000 ARG A 52 *********************** 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 146 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 1.173 Fit side-chains REVERT: A 69 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8329 (mp) REVERT: A 280 GLN cc_start: 0.7050 (OUTLIER) cc_final: 0.5435 (mp10) REVERT: A 363 LEU cc_start: 0.8305 (mp) cc_final: 0.7990 (mt) REVERT: A 410 THR cc_start: 0.8924 (p) cc_final: 0.8723 (t) REVERT: A 554 ARG cc_start: 0.7956 (ttm170) cc_final: 0.7630 (mtm110) REVERT: A 612 GLN cc_start: 0.7466 (mt0) cc_final: 0.6816 (mt0) REVERT: A 715 ASP cc_start: 0.7760 (t0) cc_final: 0.7414 (t0) REVERT: B 69 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8330 (mp) REVERT: B 280 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.5430 (mp10) REVERT: B 363 LEU cc_start: 0.8304 (mp) cc_final: 0.7989 (mt) REVERT: B 410 THR cc_start: 0.8926 (p) cc_final: 0.8724 (t) REVERT: B 554 ARG cc_start: 0.7957 (ttm170) cc_final: 0.7635 (mtm110) REVERT: B 612 GLN cc_start: 0.7471 (mt0) cc_final: 0.6818 (mt0) REVERT: B 715 ASP cc_start: 0.7756 (t0) cc_final: 0.7407 (t0) outliers start: 18 outliers final: 11 residues processed: 136 average time/residue: 0.2030 time to fit residues: 41.0033 Evaluate side-chains 135 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.065 ------------------------------------------------------------------------------- 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: 8.9990 chunk 0 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 54 optimal weight: 1.9990 chunk 16 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 75 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 107 optimal weight: 4.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.137618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.113224 restraints weight = 11833.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.112075 restraints weight = 16314.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.113597 restraints weight = 16619.936| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 10402 Z= 0.354 Angle : 0.584 5.821 14112 Z= 0.304 Chirality : 0.045 0.137 1682 Planarity : 0.004 0.034 1750 Dihedral : 5.342 43.322 1391 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.40 % Allowed : 15.56 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.21), residues: 1286 helix: -2.31 (0.17), residues: 754 sheet: -1.50 (0.92), residues: 36 loop : -1.94 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 63 HIS 0.003 0.001 HIS B 220 PHE 0.020 0.002 PHE B 130 TYR 0.027 0.002 TYR B 9 ARG 0.001 0.000 ARG A 569 *********************** 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 152 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.5776 (mp10) REVERT: A 293 GLU cc_start: 0.7282 (mt-10) cc_final: 0.6272 (tt0) REVERT: A 363 LEU cc_start: 0.8357 (mp) cc_final: 0.8023 (mt) REVERT: A 404 GLU cc_start: 0.6676 (tt0) cc_final: 0.6473 (tt0) REVERT: A 608 LEU cc_start: 0.6718 (OUTLIER) cc_final: 0.6470 (pp) REVERT: A 612 GLN cc_start: 0.7428 (mt0) cc_final: 0.6647 (mt0) REVERT: B 280 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.5771 (mp10) REVERT: B 293 GLU cc_start: 0.7286 (mt-10) cc_final: 0.6275 (tt0) REVERT: B 363 LEU cc_start: 0.8353 (mp) cc_final: 0.8019 (mt) REVERT: B 404 GLU cc_start: 0.6679 (tt0) cc_final: 0.6471 (tt0) REVERT: B 608 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6468 (pp) REVERT: B 612 GLN cc_start: 0.7426 (mt0) cc_final: 0.6642 (mt0) outliers start: 38 outliers final: 29 residues processed: 134 average time/residue: 0.2095 time to fit residues: 41.4391 Evaluate side-chains 139 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 106 time to evaluate : 1.246 ------------------------------------------------------------------------------- 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 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 99 ASP 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: 0.8980 chunk 124 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 0.0670 chunk 46 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 47 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.7318 ------------------------------------------------------------------------------- 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 = 0.141318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.116988 restraints weight = 11753.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.115810 restraints weight = 16047.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.117128 restraints weight = 15439.265| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10402 Z= 0.137 Angle : 0.467 5.085 14112 Z= 0.250 Chirality : 0.041 0.126 1682 Planarity : 0.003 0.035 1750 Dihedral : 4.836 29.903 1391 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.33 % Allowed : 17.80 % Favored : 79.87 % 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: -2.89 (0.22), residues: 1286 helix: -1.98 (0.18), residues: 758 sheet: -1.07 (0.98), residues: 36 loop : -1.60 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.003 0.000 HIS B 237 PHE 0.011 0.001 PHE B 130 TYR 0.010 0.001 TYR B 545 ARG 0.003 0.000 ARG B 52 *********************** 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 144 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.6750 (ptp90) cc_final: 0.6321 (ttp80) REVERT: A 280 GLN cc_start: 0.7221 (OUTLIER) cc_final: 0.5719 (mp10) REVERT: A 363 LEU cc_start: 0.8287 (mp) cc_final: 0.7941 (mt) REVERT: A 612 GLN cc_start: 0.7444 (mt0) cc_final: 0.6746 (mt0) REVERT: B 52 ARG cc_start: 0.6756 (ptp90) cc_final: 0.6324 (ttp80) REVERT: B 236 SER cc_start: 0.8553 (OUTLIER) cc_final: 0.8300 (m) REVERT: B 280 GLN cc_start: 0.7228 (OUTLIER) cc_final: 0.5732 (mp10) REVERT: B 363 LEU cc_start: 0.8282 (mp) cc_final: 0.7937 (mt) REVERT: B 612 GLN cc_start: 0.7450 (mt0) cc_final: 0.6754 (mt0) outliers start: 26 outliers final: 19 residues processed: 134 average time/residue: 0.1789 time to fit residues: 36.9394 Evaluate side-chains 129 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 107 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 280 GLN 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 A residue 722 MET 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 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 Chi-restraints excluded: chain B residue 722 MET 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: 1.9990 chunk 75 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 41 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 86 optimal weight: 0.0980 chunk 95 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 0.0870 overall best weight: 0.8364 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.141703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.117233 restraints weight = 11770.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.116287 restraints weight = 16194.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.117734 restraints weight = 16261.837| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10402 Z= 0.144 Angle : 0.466 5.083 14112 Z= 0.247 Chirality : 0.041 0.128 1682 Planarity : 0.003 0.038 1750 Dihedral : 4.593 18.145 1391 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.68 % Allowed : 17.71 % Favored : 79.61 % 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: -2.52 (0.22), residues: 1286 helix: -1.69 (0.18), residues: 738 sheet: -0.83 (1.02), residues: 36 loop : -1.46 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.002 0.001 HIS B 237 PHE 0.014 0.001 PHE B 130 TYR 0.012 0.001 TYR B 9 ARG 0.001 0.000 ARG A 569 *********************** 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 151 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 48 GLN cc_start: 0.6725 (tp40) cc_final: 0.6519 (tp-100) REVERT: A 52 ARG cc_start: 0.6745 (ptp90) cc_final: 0.6292 (ttp80) REVERT: A 280 GLN cc_start: 0.7137 (OUTLIER) cc_final: 0.5543 (mp10) REVERT: A 363 LEU cc_start: 0.8296 (mp) cc_final: 0.7951 (mt) REVERT: A 612 GLN cc_start: 0.7494 (mt0) cc_final: 0.6839 (mt0) REVERT: B 48 GLN cc_start: 0.6722 (tp40) cc_final: 0.6514 (tp-100) REVERT: B 52 ARG cc_start: 0.6754 (ptp90) cc_final: 0.6293 (ttp80) REVERT: B 280 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.5553 (mp10) REVERT: B 363 LEU cc_start: 0.8292 (mp) cc_final: 0.7945 (mt) REVERT: B 612 GLN cc_start: 0.7496 (mt0) cc_final: 0.6848 (mt0) outliers start: 30 outliers final: 26 residues processed: 139 average time/residue: 0.1810 time to fit residues: 38.8644 Evaluate side-chains 138 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 110 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 174 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 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 174 VAL 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: 0.0370 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 66 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 31 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.8662 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.142137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.118364 restraints weight = 11691.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.117203 restraints weight = 17570.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.118737 restraints weight = 16421.734| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10402 Z= 0.143 Angle : 0.461 5.049 14112 Z= 0.245 Chirality : 0.041 0.127 1682 Planarity : 0.003 0.036 1750 Dihedral : 4.501 18.139 1390 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.22 % Allowed : 17.26 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.23), residues: 1286 helix: -1.56 (0.19), residues: 750 sheet: -0.78 (1.02), residues: 36 loop : -1.37 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.002 0.000 HIS B 237 PHE 0.013 0.001 PHE B 130 TYR 0.020 0.001 TYR B 361 ARG 0.001 0.000 ARG A 569 *********************** 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 149 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 113 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.6715 (ptp90) cc_final: 0.6297 (ttp80) REVERT: A 280 GLN cc_start: 0.7091 (OUTLIER) cc_final: 0.5490 (mp10) REVERT: A 363 LEU cc_start: 0.8216 (mp) cc_final: 0.7856 (mt) REVERT: A 612 GLN cc_start: 0.7437 (mt0) cc_final: 0.6792 (mt0) REVERT: B 52 ARG cc_start: 0.6721 (ptp90) cc_final: 0.6299 (ttp80) REVERT: B 280 GLN cc_start: 0.7071 (OUTLIER) cc_final: 0.5473 (mp10) REVERT: B 363 LEU cc_start: 0.8214 (mp) cc_final: 0.7852 (mt) REVERT: B 612 GLN cc_start: 0.7444 (mt0) cc_final: 0.6796 (mt0) outliers start: 36 outliers final: 30 residues processed: 137 average time/residue: 0.1752 time to fit residues: 36.7502 Evaluate side-chains 142 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 1.167 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain A residue 174 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 127 VAL Chi-restraints excluded: chain B residue 174 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: 0.8980 chunk 100 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3448 r_free = 0.3448 target = 0.142279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.117603 restraints weight = 11687.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.116480 restraints weight = 16078.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.118321 restraints weight = 16381.250| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10402 Z= 0.146 Angle : 0.460 5.103 14112 Z= 0.245 Chirality : 0.041 0.126 1682 Planarity : 0.003 0.037 1750 Dihedral : 4.434 17.100 1390 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.04 % Allowed : 17.89 % 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: -2.25 (0.23), residues: 1286 helix: -1.46 (0.19), residues: 762 sheet: -0.76 (1.03), residues: 36 loop : -1.33 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.002 0.000 HIS B 237 PHE 0.012 0.001 PHE A 130 TYR 0.016 0.001 TYR B 361 ARG 0.001 0.000 ARG A 569 *********************** 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: 34 poor density : 118 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.6698 (ptp90) cc_final: 0.6243 (ttp80) REVERT: A 280 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.5499 (mp10) REVERT: A 363 LEU cc_start: 0.8188 (mp) cc_final: 0.7821 (mt) REVERT: A 612 GLN cc_start: 0.7470 (mt0) cc_final: 0.6817 (mt0) REVERT: B 52 ARG cc_start: 0.6702 (ptp90) cc_final: 0.6241 (ttp80) REVERT: B 280 GLN cc_start: 0.7101 (OUTLIER) cc_final: 0.5494 (mp10) REVERT: B 363 LEU cc_start: 0.8183 (mp) cc_final: 0.7815 (mt) REVERT: B 612 GLN cc_start: 0.7472 (mt0) cc_final: 0.6823 (mt0) outliers start: 34 outliers final: 32 residues processed: 138 average time/residue: 0.1833 time to fit residues: 38.3645 Evaluate side-chains 146 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 1.088 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain A residue 174 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 127 VAL Chi-restraints excluded: chain B residue 174 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 88 optimal weight: 4.9990 chunk 115 optimal weight: 0.0370 chunk 87 optimal weight: 3.9990 chunk 5 optimal weight: 0.0030 chunk 113 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 56 optimal weight: 0.0060 chunk 68 optimal weight: 0.1980 chunk 121 optimal weight: 0.0470 chunk 21 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 overall best weight: 0.0582 ------------------------------------------------------------------------------- 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 = 0.3486 r_free = 0.3486 target = 0.145805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.122826 restraints weight = 11565.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.122314 restraints weight = 14919.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.122840 restraints weight = 14132.269| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2668 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= 0.103 Angle : 0.437 5.228 14112 Z= 0.235 Chirality : 0.040 0.127 1682 Planarity : 0.003 0.038 1750 Dihedral : 4.134 16.972 1390 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.61 % Allowed : 19.86 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.23), residues: 1286 helix: -1.10 (0.19), residues: 760 sheet: -0.49 (1.05), residues: 36 loop : -1.22 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 63 HIS 0.002 0.000 HIS B 237 PHE 0.012 0.001 PHE A 130 TYR 0.016 0.001 TYR A 361 ARG 0.004 0.000 ARG B 312 ********************** 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 130 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.5499 (mp10) REVERT: A 363 LEU cc_start: 0.8110 (mp) cc_final: 0.7762 (mt) REVERT: A 516 ARG cc_start: 0.6649 (mmt-90) cc_final: 0.6437 (mtp180) REVERT: B 280 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.5493 (mp10) REVERT: B 363 LEU cc_start: 0.8112 (mp) cc_final: 0.7763 (mt) REVERT: B 516 ARG cc_start: 0.6648 (mmt-90) cc_final: 0.6440 (mtp180) outliers start: 18 outliers final: 16 residues processed: 119 average time/residue: 0.2006 time to fit residues: 35.5540 Evaluate side-chains 126 residues out of total 1118 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 226 LEU Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 321 MET 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 69 LEU Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 270 LEU Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 321 MET 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: 9.9990 chunk 21 optimal weight: 7.9990 chunk 22 optimal weight: 0.2980 chunk 9 optimal weight: 0.9990 chunk 90 optimal weight: 0.1980 chunk 123 optimal weight: 0.0170 chunk 37 optimal weight: 7.9990 chunk 45 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 119 optimal weight: 8.9990 overall best weight: 0.3818 ------------------------------------------------------------------------------- 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 = 0.3484 r_free = 0.3484 target = 0.145523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.122760 restraints weight = 11589.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.122367 restraints weight = 14253.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.123012 restraints weight = 13018.511| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10402 Z= 0.117 Angle : 0.453 7.082 14112 Z= 0.243 Chirality : 0.040 0.125 1682 Planarity : 0.003 0.040 1750 Dihedral : 4.083 16.514 1390 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.33 % Allowed : 19.41 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.23), residues: 1286 helix: -0.91 (0.19), residues: 760 sheet: -0.41 (1.05), residues: 36 loop : -1.17 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.002 0.000 HIS B 237 PHE 0.012 0.001 PHE A 130 TYR 0.018 0.001 TYR B 361 ARG 0.001 0.000 ARG B 312 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2738.07 seconds wall clock time: 50 minutes 9.91 seconds (3009.91 seconds total)