Starting phenix.real_space_refine on Wed Sep 25 09:11:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iet_35393/09_2024/8iet_35393.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iet_35393/09_2024/8iet_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iet_35393/09_2024/8iet_35393.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iet_35393/09_2024/8iet_35393.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iet_35393/09_2024/8iet_35393.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iet_35393/09_2024/8iet_35393.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 38 5.16 5 C 6700 2.51 5 N 1670 2.21 5 O 1776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 6.00, 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: 2.47 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: 1.10 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: 2.57 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3146 1.34 - 1.46: 2041 1.46 - 1.58: 5157 1.58 - 1.69: 0 1.69 - 1.81: 58 Bond restraints: 10402 Sorted by residual: bond pdb=" C ASP B 239 " pdb=" N PRO B 240 " ideal model delta sigma weight residual 1.331 1.394 -0.063 1.21e-02 6.83e+03 2.72e+01 bond pdb=" C ASP A 239 " pdb=" N PRO A 240 " ideal model delta sigma weight residual 1.331 1.394 -0.063 1.21e-02 6.83e+03 2.68e+01 bond pdb=" N PRO A 240 " pdb=" CD PRO A 240 " ideal model delta sigma weight residual 1.473 1.528 -0.055 1.40e-02 5.10e+03 1.56e+01 bond pdb=" N PRO B 240 " pdb=" CD PRO B 240 " ideal model delta sigma weight residual 1.473 1.527 -0.054 1.40e-02 5.10e+03 1.51e+01 bond pdb=" CA ASP B 239 " pdb=" C ASP B 239 " ideal model delta sigma weight residual 1.524 1.545 -0.021 1.26e-02 6.30e+03 2.88e+00 ... (remaining 10397 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 13872 2.78 - 5.56: 226 5.56 - 8.34: 6 8.34 - 11.12: 6 11.12 - 13.90: 2 Bond angle restraints: 14112 Sorted by residual: angle pdb=" N THR A 238 " pdb=" CA THR A 238 " pdb=" C THR A 238 " ideal model delta sigma weight residual 110.80 121.50 -10.70 2.13e+00 2.20e-01 2.52e+01 angle pdb=" N THR B 238 " pdb=" CA THR B 238 " pdb=" C THR B 238 " ideal model delta sigma weight residual 110.80 121.31 -10.51 2.13e+00 2.20e-01 2.44e+01 angle pdb=" C ASP B 239 " pdb=" N PRO B 240 " pdb=" CA PRO B 240 " ideal model delta sigma weight residual 120.11 114.59 5.52 1.12e+00 7.97e-01 2.43e+01 angle pdb=" C ASP A 239 " pdb=" N PRO A 240 " pdb=" CA PRO A 240 " ideal model delta sigma weight residual 120.11 114.60 5.51 1.12e+00 7.97e-01 2.42e+01 angle pdb=" C SER A 17 " pdb=" N THR A 18 " pdb=" CA THR A 18 " ideal model delta sigma weight residual 121.54 130.88 -9.34 1.91e+00 2.74e-01 2.39e+01 ... (remaining 14107 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.29: 5425 16.29 - 32.58: 627 32.58 - 48.87: 105 48.87 - 65.16: 15 65.16 - 81.45: 4 Dihedral angle restraints: 6176 sinusoidal: 2400 harmonic: 3776 Sorted by residual: dihedral pdb=" CA LEU A 435 " pdb=" C LEU A 435 " pdb=" N GLN A 436 " pdb=" CA GLN A 436 " ideal model delta harmonic sigma weight residual -180.00 -152.67 -27.33 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA LEU B 435 " pdb=" C LEU B 435 " pdb=" N GLN B 436 " pdb=" CA GLN B 436 " ideal model delta harmonic sigma weight residual -180.00 -152.67 -27.33 0 5.00e+00 4.00e-02 2.99e+01 dihedral pdb=" CA SER A 438 " pdb=" C SER A 438 " pdb=" N VAL A 439 " pdb=" CA VAL A 439 " ideal model delta harmonic sigma weight residual 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 6173 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1489 0.079 - 0.157: 185 0.157 - 0.236: 4 0.236 - 0.315: 0 0.315 - 0.393: 4 Chirality restraints: 1682 Sorted by residual: chirality pdb=" CA ASP B 239 " pdb=" N ASP B 239 " pdb=" C ASP B 239 " pdb=" CB ASP B 239 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.87e+00 chirality pdb=" CA ASP A 239 " pdb=" N ASP A 239 " pdb=" C ASP A 239 " pdb=" CB ASP A 239 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" CA THR B 238 " pdb=" N THR B 238 " pdb=" C THR B 238 " pdb=" CB THR B 238 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 1679 not shown) Planarity restraints: 1750 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE B 100 " 0.049 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO B 101 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 101 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 101 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 100 " 0.049 5.00e-02 4.00e+02 7.32e-02 8.57e+00 pdb=" N PRO A 101 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 433 " 0.039 5.00e-02 4.00e+02 5.79e-02 5.36e+00 pdb=" N PRO A 434 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 434 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 434 " 0.032 5.00e-02 4.00e+02 ... (remaining 1747 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1250 2.75 - 3.28: 9001 3.28 - 3.82: 15215 3.82 - 4.36: 19244 4.36 - 4.90: 33420 Nonbonded interactions: 78130 Sorted by model distance: nonbonded pdb=" O THR A 238 " pdb=" O ASP A 239 " model vdw 2.207 3.040 nonbonded pdb=" O THR B 238 " pdb=" O ASP B 239 " model vdw 2.277 3.040 nonbonded pdb=" O GLY B 487 " pdb=" OG SER B 491 " model vdw 2.337 3.040 nonbonded pdb=" O GLY A 487 " pdb=" OG SER A 491 " model vdw 2.337 3.040 nonbonded pdb=" OD1 ASP A 465 " pdb=" OH TYR B 697 " model vdw 2.339 3.040 ... (remaining 78125 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.350 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: 0.080 Set scattering table: 0.090 Process input model: 24.170 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.050 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 5 poor density : 168 time to evaluate : 1.137 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: 0.2308 time to fit residues: 54.9695 Evaluate side-chains 113 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 110 time to evaluate : 1.111 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 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 fitting. rotamer outliers: 19 poor density : 133 time to evaluate : 1.153 Fit side-chains REVERT: A 55 LEU cc_start: 0.8302 (mp) cc_final: 0.7862 (tt) REVERT: A 293 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6165 (tt0) REVERT: A 363 LEU cc_start: 0.8152 (mp) cc_final: 0.7800 (mp) REVERT: A 612 GLN cc_start: 0.7521 (mt0) cc_final: 0.6747 (mt0) REVERT: B 55 LEU cc_start: 0.8300 (mp) cc_final: 0.7860 (tt) REVERT: B 293 GLU cc_start: 0.7243 (mt-10) cc_final: 0.6164 (tt0) REVERT: B 363 LEU cc_start: 0.8147 (mp) cc_final: 0.7795 (mp) REVERT: B 612 GLN cc_start: 0.7530 (mt0) cc_final: 0.6757 (mt0) outliers start: 19 outliers final: 9 residues processed: 141 average time/residue: 0.1717 time to fit residues: 37.2300 Evaluate side-chains 124 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 0.983 ------------------------------------------------------------------------------- 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 65 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 32 optimal weight: 0.3980 chunk 118 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 105 optimal weight: 7.9990 chunk 117 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 overall best weight: 2.8786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10402 Z= 0.365 Angle : 0.624 6.970 14112 Z= 0.325 Chirality : 0.046 0.143 1682 Planarity : 0.004 0.044 1750 Dihedral : 5.925 57.631 1391 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.60 % Favored : 94.32 % Rotamer: Outliers : 2.86 % Allowed : 15.21 % Favored : 81.93 % 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: -4.31 (0.20), residues: 1286 helix: -3.01 (0.15), residues: 748 sheet: -2.02 (0.88), residues: 36 loop : -2.39 (0.25), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.006 0.001 HIS B 237 PHE 0.022 0.002 PHE B 130 TYR 0.030 0.002 TYR B 9 ARG 0.003 0.000 ARG A 312 *********************** 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 145 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 113 time to evaluate : 1.188 Fit side-chains REVERT: A 280 GLN cc_start: 0.7317 (OUTLIER) cc_final: 0.5770 (mp10) REVERT: A 293 GLU cc_start: 0.7370 (mt-10) cc_final: 0.6385 (tt0) REVERT: A 363 LEU cc_start: 0.8281 (mp) cc_final: 0.7942 (mt) REVERT: A 554 ARG cc_start: 0.7964 (ttm170) cc_final: 0.7622 (mtm110) REVERT: A 612 GLN cc_start: 0.7458 (mt0) cc_final: 0.6742 (mt0) REVERT: B 280 GLN cc_start: 0.7318 (OUTLIER) cc_final: 0.5776 (mp10) REVERT: B 293 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6396 (tt0) REVERT: B 363 LEU cc_start: 0.8273 (mp) cc_final: 0.7932 (mt) REVERT: B 554 ARG cc_start: 0.7965 (ttm170) cc_final: 0.7620 (mtm110) REVERT: B 612 GLN cc_start: 0.7461 (mt0) cc_final: 0.6745 (mt0) outliers start: 32 outliers final: 23 residues processed: 130 average time/residue: 0.2161 time to fit residues: 40.7746 Evaluate side-chains 130 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 105 time to evaluate : 1.048 ------------------------------------------------------------------------------- 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 99 ASP Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 298 VAL Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 517 THR Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 661 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 99 ASP Chi-restraints excluded: chain B residue 174 VAL Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 661 VAL 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 116 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 56 optimal weight: 0.0570 chunk 79 optimal weight: 3.9990 chunk 118 optimal weight: 0.6980 chunk 125 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1840 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= 0.125 Angle : 0.483 5.174 14112 Z= 0.259 Chirality : 0.041 0.132 1682 Planarity : 0.003 0.037 1750 Dihedral : 5.336 56.205 1391 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.06 % Allowed : 16.99 % Favored : 80.95 % 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: -3.50 (0.21), residues: 1286 helix: -2.43 (0.17), residues: 758 sheet: -1.21 (0.98), residues: 36 loop : -1.94 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.004 0.000 HIS B 237 PHE 0.013 0.001 PHE A 562 TYR 0.008 0.001 TYR B 9 ARG 0.002 0.000 ARG A 569 *********************** 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 144 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8428 (mp) REVERT: A 280 GLN cc_start: 0.7231 (OUTLIER) cc_final: 0.5752 (mp10) REVERT: A 363 LEU cc_start: 0.8285 (mp) cc_final: 0.7960 (mt) REVERT: A 554 ARG cc_start: 0.7958 (ttm170) cc_final: 0.7615 (mtm110) REVERT: A 612 GLN cc_start: 0.7407 (mt0) cc_final: 0.6710 (mt0) REVERT: A 715 ASP cc_start: 0.7773 (t0) cc_final: 0.7553 (t0) REVERT: B 69 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8425 (mp) REVERT: B 280 GLN cc_start: 0.7235 (OUTLIER) cc_final: 0.5758 (mp10) REVERT: B 363 LEU cc_start: 0.8277 (mp) cc_final: 0.7953 (mt) REVERT: B 554 ARG cc_start: 0.7960 (ttm170) cc_final: 0.7617 (mtm110) REVERT: B 612 GLN cc_start: 0.7418 (mt0) cc_final: 0.6735 (mt0) REVERT: B 715 ASP cc_start: 0.7777 (t0) cc_final: 0.7550 (t0) outliers start: 23 outliers final: 14 residues processed: 131 average time/residue: 0.2008 time to fit residues: 39.5013 Evaluate side-chains 129 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 99 ASP Chi-restraints excluded: chain A residue 233 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 321 MET 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 99 ASP 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 337 GLN 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 104 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 1 optimal weight: 0.0270 chunk 93 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 107 optimal weight: 0.0020 chunk 86 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 chunk 112 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 overall best weight: 1.5850 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10402 Z= 0.220 Angle : 0.510 5.095 14112 Z= 0.268 Chirality : 0.042 0.129 1682 Planarity : 0.003 0.033 1750 Dihedral : 5.257 52.687 1391 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.77 % Allowed : 17.53 % Favored : 79.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.22), residues: 1286 helix: -2.19 (0.18), residues: 746 sheet: -1.40 (0.94), residues: 36 loop : -1.78 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 63 HIS 0.002 0.001 HIS A 220 PHE 0.017 0.001 PHE A 130 TYR 0.018 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 146 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 115 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.7289 (OUTLIER) cc_final: 0.5822 (mp10) REVERT: A 363 LEU cc_start: 0.8287 (mp) cc_final: 0.7916 (mt) REVERT: A 612 GLN cc_start: 0.7447 (mt0) cc_final: 0.6737 (mt0) REVERT: B 280 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.5826 (mp10) REVERT: B 363 LEU cc_start: 0.8276 (mp) cc_final: 0.7904 (mt) REVERT: B 612 GLN cc_start: 0.7460 (mt0) cc_final: 0.6742 (mt0) outliers start: 31 outliers final: 24 residues processed: 132 average time/residue: 0.1813 time to fit residues: 36.7406 Evaluate side-chains 137 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 THR Chi-restraints excluded: chain A residue 99 ASP Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 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 517 THR Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain A residue 712 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 99 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 233 THR Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 321 MET Chi-restraints excluded: chain B residue 517 THR Chi-restraints excluded: chain B residue 640 GLU Chi-restraints excluded: chain B residue 712 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 73 optimal weight: 0.4980 chunk 31 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 104 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10402 Z= 0.336 Angle : 0.576 6.412 14112 Z= 0.299 Chirality : 0.045 0.136 1682 Planarity : 0.004 0.036 1750 Dihedral : 5.488 47.416 1391 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.29 % Favored : 94.56 % Rotamer: Outliers : 4.20 % Allowed : 17.26 % 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: -3.24 (0.21), residues: 1286 helix: -2.18 (0.18), residues: 746 sheet: -1.96 (0.88), residues: 36 loop : -1.84 (0.25), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 63 HIS 0.003 0.001 HIS B 220 PHE 0.019 0.001 PHE A 130 TYR 0.028 0.002 TYR B 9 ARG 0.001 0.000 ARG A 539 *********************** 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 162 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 115 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.7364 (OUTLIER) cc_final: 0.5905 (mp10) REVERT: A 363 LEU cc_start: 0.8316 (mp) cc_final: 0.7915 (mt) REVERT: A 612 GLN cc_start: 0.7388 (mt0) cc_final: 0.6734 (mt0) REVERT: B 280 GLN cc_start: 0.7359 (OUTLIER) cc_final: 0.5906 (mp10) REVERT: B 293 GLU cc_start: 0.7340 (mt-10) cc_final: 0.6313 (tt0) REVERT: B 363 LEU cc_start: 0.8307 (mp) cc_final: 0.7909 (mt) REVERT: B 612 GLN cc_start: 0.7395 (mt0) cc_final: 0.6742 (mt0) outliers start: 47 outliers final: 39 residues processed: 148 average time/residue: 0.1535 time to fit residues: 35.4950 Evaluate side-chains 148 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 107 time to evaluate : 1.103 ------------------------------------------------------------------------------- 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 99 ASP 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 233 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 243 ILE 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 320 ASP 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 640 GLU Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 661 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 99 ASP 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 233 THR Chi-restraints excluded: chain B residue 236 SER Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 243 ILE Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 320 ASP 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 640 GLU Chi-restraints excluded: chain B residue 641 VAL Chi-restraints excluded: chain B residue 661 VAL Chi-restraints excluded: chain B residue 712 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 71 optimal weight: 9.9990 chunk 91 optimal weight: 0.9990 chunk 105 optimal weight: 0.0270 chunk 70 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 78 optimal weight: 0.0060 chunk 76 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.5454 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2228 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= 0.122 Angle : 0.460 5.099 14112 Z= 0.245 Chirality : 0.040 0.130 1682 Planarity : 0.003 0.034 1750 Dihedral : 4.916 36.207 1391 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.77 % Allowed : 17.80 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.70 (0.22), residues: 1286 helix: -1.79 (0.19), residues: 740 sheet: -1.30 (0.97), residues: 36 loop : -1.57 (0.26), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 63 HIS 0.003 0.000 HIS B 237 PHE 0.010 0.001 PHE A 130 TYR 0.008 0.001 TYR A 361 ARG 0.002 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 145 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 114 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.7260 (OUTLIER) cc_final: 0.5836 (mp10) REVERT: A 363 LEU cc_start: 0.8232 (mp) cc_final: 0.7875 (mt) REVERT: A 612 GLN cc_start: 0.7408 (mt0) cc_final: 0.6752 (mt0) REVERT: B 280 GLN cc_start: 0.7255 (OUTLIER) cc_final: 0.5835 (mp10) REVERT: B 363 LEU cc_start: 0.8227 (mp) cc_final: 0.7869 (mt) REVERT: B 612 GLN cc_start: 0.7418 (mt0) cc_final: 0.6759 (mt0) outliers start: 31 outliers final: 24 residues processed: 136 average time/residue: 0.1762 time to fit residues: 37.5499 Evaluate side-chains 132 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 106 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 298 VAL 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 712 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 226 LEU 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 640 GLU Chi-restraints excluded: chain B residue 641 VAL 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 50 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 85 optimal weight: 0.0970 chunk 61 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 120 optimal weight: 8.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 B 454 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10402 Z= 0.132 Angle : 0.455 5.119 14112 Z= 0.242 Chirality : 0.040 0.129 1682 Planarity : 0.003 0.033 1750 Dihedral : 4.551 18.669 1391 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.59 % Allowed : 18.16 % Favored : 79.25 % 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: -2.35 (0.23), residues: 1286 helix: -1.52 (0.19), residues: 738 sheet: -1.08 (1.00), residues: 36 loop : -1.41 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.002 0.000 HIS B 237 PHE 0.012 0.001 PHE A 130 TYR 0.011 0.001 TYR A 545 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 142 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 113 time to evaluate : 0.936 Fit side-chains REVERT: A 52 ARG cc_start: 0.6736 (ptt-90) cc_final: 0.6352 (ptp90) REVERT: A 280 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.5573 (mp10) REVERT: A 363 LEU cc_start: 0.8216 (mp) cc_final: 0.7849 (mt) REVERT: A 612 GLN cc_start: 0.7422 (mt0) cc_final: 0.6748 (mt0) REVERT: B 52 ARG cc_start: 0.6745 (ptt-90) cc_final: 0.6348 (ptp90) REVERT: B 280 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.5572 (mp10) REVERT: B 363 LEU cc_start: 0.8207 (mp) cc_final: 0.7841 (mt) REVERT: B 612 GLN cc_start: 0.7427 (mt0) cc_final: 0.6756 (mt0) outliers start: 29 outliers final: 26 residues processed: 133 average time/residue: 0.1687 time to fit residues: 34.4563 Evaluate side-chains 137 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 109 time to evaluate : 0.931 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 298 VAL 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 712 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 298 VAL 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 712 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 3.9990 chunk 116 optimal weight: 0.7980 chunk 120 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 110 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 123 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 454 GLN B 48 GLN B 454 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2431 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= 0.136 Angle : 0.462 5.178 14112 Z= 0.247 Chirality : 0.041 0.126 1682 Planarity : 0.003 0.037 1750 Dihedral : 4.464 17.988 1390 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.86 % Allowed : 18.43 % Favored : 78.71 % 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: -2.23 (0.23), residues: 1286 helix: -1.41 (0.19), residues: 738 sheet: -0.98 (1.01), residues: 36 loop : -1.40 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 63 HIS 0.002 0.000 HIS B 237 PHE 0.012 0.001 PHE B 130 TYR 0.010 0.001 TYR A 9 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 142 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 110 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.5517 (mp10) REVERT: A 363 LEU cc_start: 0.8163 (mp) cc_final: 0.7792 (mt) REVERT: A 612 GLN cc_start: 0.7428 (mt0) cc_final: 0.6750 (mt0) REVERT: B 280 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.5514 (mp10) REVERT: B 363 LEU cc_start: 0.8154 (mp) cc_final: 0.7782 (mt) REVERT: B 612 GLN cc_start: 0.7438 (mt0) cc_final: 0.6755 (mt0) outliers start: 32 outliers final: 28 residues processed: 132 average time/residue: 0.1774 time to fit residues: 36.1651 Evaluate side-chains 135 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 105 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 127 VAL Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 298 VAL 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 712 THR Chi-restraints excluded: chain B residue 18 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 202 VAL Chi-restraints excluded: chain B residue 226 LEU Chi-restraints excluded: chain B residue 241 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 280 GLN Chi-restraints excluded: chain B residue 298 VAL 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 712 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 0.9990 chunk 58 optimal weight: 0.3980 chunk 85 optimal weight: 0.5980 chunk 129 optimal weight: 3.9990 chunk 119 optimal weight: 0.0770 chunk 103 optimal weight: 0.0000 chunk 10 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 63 optimal weight: 0.0770 chunk 81 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 overall best weight: 0.2300 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2658 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= 0.107 Angle : 0.447 5.270 14112 Z= 0.240 Chirality : 0.040 0.126 1682 Planarity : 0.003 0.038 1750 Dihedral : 4.156 17.221 1390 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.70 % Allowed : 19.50 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.23), residues: 1286 helix: -1.12 (0.19), residues: 764 sheet: -0.75 (1.03), residues: 36 loop : -1.25 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.002 0.000 HIS B 237 PHE 0.011 0.001 PHE A 130 TYR 0.009 0.001 TYR B 545 ARG 0.001 0.000 ARG A 579 ********************** 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 128 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 280 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.5468 (mp10) REVERT: A 363 LEU cc_start: 0.7971 (mp) cc_final: 0.7633 (mt) REVERT: B 280 GLN cc_start: 0.6921 (OUTLIER) cc_final: 0.5410 (mp10) REVERT: B 363 LEU cc_start: 0.7958 (mp) cc_final: 0.7627 (mt) outliers start: 19 outliers final: 17 residues processed: 120 average time/residue: 0.1793 time to fit residues: 32.9806 Evaluate side-chains 115 residues out of total 1118 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 96 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 280 GLN Chi-restraints excluded: chain A residue 320 ASP Chi-restraints excluded: chain A residue 321 MET Chi-restraints excluded: chain A residue 641 VAL Chi-restraints excluded: chain A residue 661 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 127 VAL Chi-restraints excluded: chain B residue 226 LEU 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 641 VAL Chi-restraints excluded: chain B residue 661 VAL 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 31 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 103 optimal weight: 0.0370 chunk 43 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 19 optimal weight: 0.0870 chunk 90 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.5036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.144912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.120592 restraints weight = 11514.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.119510 restraints weight = 14173.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.120699 restraints weight = 14999.791| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.2701 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= 0.119 Angle : 0.453 5.289 14112 Z= 0.242 Chirality : 0.040 0.127 1682 Planarity : 0.003 0.040 1750 Dihedral : 4.146 16.427 1390 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.15 % Allowed : 19.50 % Favored : 78.35 % 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: -1.73 (0.23), residues: 1286 helix: -0.96 (0.19), residues: 756 sheet: -0.65 (1.03), residues: 36 loop : -1.25 (0.27), residues: 494 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 0.014 0.001 PHE A 313 TYR 0.018 0.001 TYR B 361 ARG 0.004 0.000 ARG A 516 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1861.41 seconds wall clock time: 37 minutes 30.31 seconds (2250.31 seconds total)