Starting phenix.real_space_refine on Thu Mar 5 06:52:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u88_20682/03_2026/6u88_20682_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u88_20682/03_2026/6u88_20682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6u88_20682/03_2026/6u88_20682_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u88_20682/03_2026/6u88_20682_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u88_20682/03_2026/6u88_20682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u88_20682/03_2026/6u88_20682.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 13116 2.51 5 N 3328 2.21 5 O 3448 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20004 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4978 Classifications: {'peptide': 611} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 589} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'P0T': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 4.12, per 1000 atoms: 0.21 Number of scatterers: 20004 At special positions: 0 Unit cell: (124.02, 124.02, 113.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 3448 8.00 N 3328 7.00 C 13116 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 882.5 milliseconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4616 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 4 sheets defined 59.2% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 76 through 87 removed outlier: 3.841A pdb=" N LEU A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 103 Processing helix chain 'A' and resid 119 through 127 Processing helix chain 'A' and resid 135 through 146 Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 176 through 185 removed outlier: 3.602A pdb=" N VAL A 180 " --> pdb=" O SER A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 219 Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 248 through 256 Processing helix chain 'A' and resid 260 through 282 removed outlier: 3.700A pdb=" N LEU A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 305 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 355 through 363 Processing helix chain 'A' and resid 377 through 413 removed outlier: 5.507A pdb=" N SER A 391 " --> pdb=" O ASP A 387 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N ARG A 392 " --> pdb=" O ARG A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 459 Processing helix chain 'A' and resid 463 through 467 removed outlier: 3.596A pdb=" N PHE A 467 " --> pdb=" O TRP A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 492 Processing helix chain 'A' and resid 496 through 512 removed outlier: 4.071A pdb=" N LEU A 500 " --> pdb=" O TRP A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 518 removed outlier: 3.819A pdb=" N THR A 516 " --> pdb=" O LEU A 513 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG A 517 " --> pdb=" O TYR A 514 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY A 518 " --> pdb=" O TYR A 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 513 through 518' Processing helix chain 'A' and resid 519 through 559 removed outlier: 3.608A pdb=" N LYS A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL A 532 " --> pdb=" O MET A 528 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A 533 " --> pdb=" O ILE A 529 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU A 534 " --> pdb=" O GLN A 530 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG A 535 " --> pdb=" O LYS A 531 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP A 536 " --> pdb=" O VAL A 532 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU A 538 " --> pdb=" O LEU A 534 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ARG A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 542 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA A 554 " --> pdb=" O GLY A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 606 removed outlier: 4.274A pdb=" N PHE A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR A 604 " --> pdb=" O LEU A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 618 through 651 removed outlier: 4.031A pdb=" N VAL A 649 " --> pdb=" O MET A 645 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASN A 650 " --> pdb=" O SER A 646 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N HIS A 651 " --> pdb=" O GLU A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 672 Processing helix chain 'B' and resid 76 through 87 removed outlier: 3.841A pdb=" N LEU B 80 " --> pdb=" O ASP B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 103 Processing helix chain 'B' and resid 119 through 127 Processing helix chain 'B' and resid 135 through 146 Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 176 through 185 removed outlier: 3.603A pdb=" N VAL B 180 " --> pdb=" O SER B 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 219 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 248 through 256 Processing helix chain 'B' and resid 260 through 282 removed outlier: 3.701A pdb=" N LEU B 266 " --> pdb=" O GLU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 Processing helix chain 'B' and resid 307 through 316 Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 377 through 413 removed outlier: 5.506A pdb=" N SER B 391 " --> pdb=" O ASP B 387 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ARG B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 459 Processing helix chain 'B' and resid 463 through 467 removed outlier: 3.596A pdb=" N PHE B 467 " --> pdb=" O TRP B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 492 Processing helix chain 'B' and resid 496 through 512 removed outlier: 4.071A pdb=" N LEU B 500 " --> pdb=" O TRP B 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 518 removed outlier: 3.819A pdb=" N THR B 516 " --> pdb=" O LEU B 513 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG B 517 " --> pdb=" O TYR B 514 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 518 " --> pdb=" O TYR B 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 513 through 518' Processing helix chain 'B' and resid 519 through 559 removed outlier: 3.609A pdb=" N LYS B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N VAL B 532 " --> pdb=" O MET B 528 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE B 533 " --> pdb=" O ILE B 529 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU B 534 " --> pdb=" O GLN B 530 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ARG B 535 " --> pdb=" O LYS B 531 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP B 536 " --> pdb=" O VAL B 532 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU B 538 " --> pdb=" O LEU B 534 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG B 539 " --> pdb=" O ARG B 535 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU B 542 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 543 " --> pdb=" O ARG B 539 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA B 554 " --> pdb=" O GLY B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 592 through 606 removed outlier: 4.274A pdb=" N PHE B 603 " --> pdb=" O GLU B 599 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR B 604 " --> pdb=" O LEU B 600 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 651 removed outlier: 4.031A pdb=" N VAL B 649 " --> pdb=" O MET B 645 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN B 650 " --> pdb=" O SER B 646 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N HIS B 651 " --> pdb=" O GLU B 647 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 672 Processing helix chain 'C' and resid 76 through 87 removed outlier: 3.841A pdb=" N LEU C 80 " --> pdb=" O ASP C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 103 Processing helix chain 'C' and resid 119 through 127 Processing helix chain 'C' and resid 135 through 146 Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 176 through 185 removed outlier: 3.602A pdb=" N VAL C 180 " --> pdb=" O SER C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 219 Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 248 through 256 Processing helix chain 'C' and resid 260 through 282 removed outlier: 3.700A pdb=" N LEU C 266 " --> pdb=" O GLU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 Processing helix chain 'C' and resid 307 through 316 Processing helix chain 'C' and resid 355 through 363 Processing helix chain 'C' and resid 377 through 413 removed outlier: 5.507A pdb=" N SER C 391 " --> pdb=" O ASP C 387 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ARG C 392 " --> pdb=" O ARG C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 459 Processing helix chain 'C' and resid 463 through 467 removed outlier: 3.597A pdb=" N PHE C 467 " --> pdb=" O TRP C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 492 Processing helix chain 'C' and resid 496 through 512 removed outlier: 4.071A pdb=" N LEU C 500 " --> pdb=" O TRP C 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 518 removed outlier: 3.819A pdb=" N THR C 516 " --> pdb=" O LEU C 513 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG C 517 " --> pdb=" O TYR C 514 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY C 518 " --> pdb=" O TYR C 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 513 through 518' Processing helix chain 'C' and resid 519 through 559 removed outlier: 3.609A pdb=" N LYS C 531 " --> pdb=" O VAL C 527 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL C 532 " --> pdb=" O MET C 528 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE C 533 " --> pdb=" O ILE C 529 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU C 534 " --> pdb=" O GLN C 530 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG C 535 " --> pdb=" O LYS C 531 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP C 536 " --> pdb=" O VAL C 532 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU C 538 " --> pdb=" O LEU C 534 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG C 539 " --> pdb=" O ARG C 535 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL C 543 " --> pdb=" O ARG C 539 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N ALA C 554 " --> pdb=" O GLY C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 592 through 606 removed outlier: 4.274A pdb=" N PHE C 603 " --> pdb=" O GLU C 599 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N THR C 604 " --> pdb=" O LEU C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 618 through 651 removed outlier: 4.031A pdb=" N VAL C 649 " --> pdb=" O MET C 645 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASN C 650 " --> pdb=" O SER C 646 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N HIS C 651 " --> pdb=" O GLU C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 672 Processing helix chain 'D' and resid 76 through 87 removed outlier: 3.842A pdb=" N LEU D 80 " --> pdb=" O ASP D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 103 Processing helix chain 'D' and resid 119 through 127 Processing helix chain 'D' and resid 135 through 146 Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 176 through 185 removed outlier: 3.603A pdb=" N VAL D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 219 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 248 through 256 Processing helix chain 'D' and resid 260 through 282 removed outlier: 3.701A pdb=" N LEU D 266 " --> pdb=" O GLU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 305 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 355 through 363 Processing helix chain 'D' and resid 377 through 413 removed outlier: 5.507A pdb=" N SER D 391 " --> pdb=" O ASP D 387 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ARG D 392 " --> pdb=" O ARG D 388 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 459 Processing helix chain 'D' and resid 463 through 467 removed outlier: 3.597A pdb=" N PHE D 467 " --> pdb=" O TRP D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 492 Processing helix chain 'D' and resid 496 through 512 removed outlier: 4.072A pdb=" N LEU D 500 " --> pdb=" O TRP D 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 removed outlier: 3.820A pdb=" N THR D 516 " --> pdb=" O LEU D 513 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG D 517 " --> pdb=" O TYR D 514 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY D 518 " --> pdb=" O TYR D 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 513 through 518' Processing helix chain 'D' and resid 519 through 559 removed outlier: 3.608A pdb=" N LYS D 531 " --> pdb=" O VAL D 527 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N VAL D 532 " --> pdb=" O MET D 528 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE D 533 " --> pdb=" O ILE D 529 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N LEU D 534 " --> pdb=" O GLN D 530 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP D 536 " --> pdb=" O VAL D 532 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU D 538 " --> pdb=" O LEU D 534 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ARG D 539 " --> pdb=" O ARG D 535 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU D 542 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL D 543 " --> pdb=" O ARG D 539 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA D 554 " --> pdb=" O GLY D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 592 through 606 removed outlier: 4.274A pdb=" N PHE D 603 " --> pdb=" O GLU D 599 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N THR D 604 " --> pdb=" O LEU D 600 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 651 removed outlier: 4.030A pdb=" N VAL D 649 " --> pdb=" O MET D 645 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N ASN D 650 " --> pdb=" O SER D 646 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N HIS D 651 " --> pdb=" O GLU D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 672 Processing sheet with id=AA1, first strand: chain 'A' and resid 329 through 335 removed outlier: 6.755A pdb=" N VAL A 340 " --> pdb=" O GLU A 332 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N CYS A 334 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N VAL A 338 " --> pdb=" O CYS A 334 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 329 through 335 removed outlier: 6.756A pdb=" N VAL B 340 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N CYS B 334 " --> pdb=" O VAL B 338 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL B 338 " --> pdb=" O CYS B 334 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 329 through 335 removed outlier: 6.756A pdb=" N VAL C 340 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N CYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL C 338 " --> pdb=" O CYS C 334 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 329 through 335 removed outlier: 6.756A pdb=" N VAL D 340 " --> pdb=" O GLU D 332 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N CYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VAL D 338 " --> pdb=" O CYS D 334 " (cutoff:3.500A) 1044 hydrogen bonds defined for protein. 3096 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.10 Time building geometry restraints manager: 2.08 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: 6127 1.34 - 1.46: 5154 1.46 - 1.59: 9059 1.59 - 1.71: 0 1.71 - 1.83: 172 Bond restraints: 20512 Sorted by residual: bond pdb=" C04 P0T C1001 " pdb=" C08 P0T C1001 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.28e+00 bond pdb=" C04 P0T D1001 " pdb=" C08 P0T D1001 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.22e+00 bond pdb=" C04 P0T A1001 " pdb=" C08 P0T A1001 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.20e+00 bond pdb=" C04 P0T B1001 " pdb=" C08 P0T B1001 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C15 P0T A1001 " pdb=" C18 P0T A1001 " ideal model delta sigma weight residual 1.503 1.552 -0.049 2.00e-02 2.50e+03 6.04e+00 ... (remaining 20507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 26385 2.08 - 4.15: 1186 4.15 - 6.23: 171 6.23 - 8.31: 46 8.31 - 10.39: 28 Bond angle restraints: 27816 Sorted by residual: angle pdb=" N TYR A 634 " pdb=" CA TYR A 634 " pdb=" C TYR A 634 " ideal model delta sigma weight residual 111.14 106.84 4.30 1.08e+00 8.57e-01 1.58e+01 angle pdb=" N TYR C 634 " pdb=" CA TYR C 634 " pdb=" C TYR C 634 " ideal model delta sigma weight residual 111.14 106.85 4.29 1.08e+00 8.57e-01 1.58e+01 angle pdb=" N TYR B 634 " pdb=" CA TYR B 634 " pdb=" C TYR B 634 " ideal model delta sigma weight residual 111.14 106.85 4.29 1.08e+00 8.57e-01 1.58e+01 angle pdb=" N TYR D 634 " pdb=" CA TYR D 634 " pdb=" C TYR D 634 " ideal model delta sigma weight residual 111.14 106.85 4.29 1.08e+00 8.57e-01 1.58e+01 angle pdb=" C03 P0T A1001 " pdb=" C04 P0T A1001 " pdb=" C08 P0T A1001 " ideal model delta sigma weight residual 111.12 120.59 -9.47 3.00e+00 1.11e-01 9.96e+00 ... (remaining 27811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.24: 10818 20.24 - 40.47: 1066 40.47 - 60.71: 156 60.71 - 80.94: 36 80.94 - 101.18: 12 Dihedral angle restraints: 12088 sinusoidal: 4944 harmonic: 7144 Sorted by residual: dihedral pdb=" CA VAL C 652 " pdb=" C VAL C 652 " pdb=" N ALA C 653 " pdb=" CA ALA C 653 " ideal model delta harmonic sigma weight residual -180.00 -151.74 -28.26 0 5.00e+00 4.00e-02 3.20e+01 dihedral pdb=" CA VAL D 652 " pdb=" C VAL D 652 " pdb=" N ALA D 653 " pdb=" CA ALA D 653 " ideal model delta harmonic sigma weight residual -180.00 -151.78 -28.22 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA VAL B 652 " pdb=" C VAL B 652 " pdb=" N ALA B 653 " pdb=" CA ALA B 653 " ideal model delta harmonic sigma weight residual -180.00 -151.81 -28.19 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 12085 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2047 0.053 - 0.105: 861 0.105 - 0.158: 140 0.158 - 0.210: 53 0.210 - 0.263: 15 Chirality restraints: 3116 Sorted by residual: chirality pdb=" CB VAL B 652 " pdb=" CA VAL B 652 " pdb=" CG1 VAL B 652 " pdb=" CG2 VAL B 652 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CB VAL A 652 " pdb=" CA VAL A 652 " pdb=" CG1 VAL A 652 " pdb=" CG2 VAL A 652 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CB VAL C 652 " pdb=" CA VAL C 652 " pdb=" CG1 VAL C 652 " pdb=" CG2 VAL C 652 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 3113 not shown) Planarity restraints: 3428 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 725 " 0.063 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO A 726 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO A 726 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 726 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 725 " -0.063 5.00e-02 4.00e+02 9.54e-02 1.46e+01 pdb=" N PRO C 726 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO C 726 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 726 " -0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 725 " -0.063 5.00e-02 4.00e+02 9.54e-02 1.46e+01 pdb=" N PRO B 726 " 0.165 5.00e-02 4.00e+02 pdb=" CA PRO B 726 " -0.051 5.00e-02 4.00e+02 pdb=" CD PRO B 726 " -0.051 5.00e-02 4.00e+02 ... (remaining 3425 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 6571 2.84 - 3.36: 17484 3.36 - 3.87: 34128 3.87 - 4.39: 38551 4.39 - 4.90: 66564 Nonbonded interactions: 163298 Sorted by model distance: nonbonded pdb=" O SER B 466 " pdb=" OG SER B 470 " model vdw 2.328 3.040 nonbonded pdb=" O SER C 466 " pdb=" OG SER C 470 " model vdw 2.329 3.040 nonbonded pdb=" O SER D 466 " pdb=" OG SER D 470 " model vdw 2.329 3.040 nonbonded pdb=" O SER A 466 " pdb=" OG SER A 470 " model vdw 2.329 3.040 nonbonded pdb=" O SER D 470 " pdb=" OG SER D 470 " model vdw 2.333 3.040 ... (remaining 163293 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 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: 0.210 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 17.070 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.009 0.084 20512 Z= 0.379 Angle : 1.052 10.385 27816 Z= 0.553 Chirality : 0.059 0.263 3116 Planarity : 0.009 0.095 3428 Dihedral : 16.098 101.178 7472 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.74 % Allowed : 10.70 % Favored : 88.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.92 (0.11), residues: 2412 helix: -3.13 (0.08), residues: 1456 sheet: -3.31 (0.36), residues: 124 loop : -3.12 (0.14), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 458 TYR 0.017 0.003 TYR C 228 PHE 0.021 0.003 PHE A 209 TRP 0.018 0.002 TRP B 454 HIS 0.011 0.002 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00896 (20512) covalent geometry : angle 1.05204 (27816) hydrogen bonds : bond 0.12574 ( 1044) hydrogen bonds : angle 7.05999 ( 3096) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 359 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 383 GLN cc_start: 0.7791 (tp40) cc_final: 0.7512 (tt0) REVERT: A 591 ARG cc_start: 0.8136 (ptm160) cc_final: 0.7711 (mmt-90) REVERT: A 595 ASP cc_start: 0.7405 (m-30) cc_final: 0.6975 (t0) REVERT: A 617 ARG cc_start: 0.7712 (ttt180) cc_final: 0.7390 (ttt180) REVERT: A 632 LEU cc_start: 0.8830 (mt) cc_final: 0.8532 (mt) REVERT: A 634 TYR cc_start: 0.8050 (OUTLIER) cc_final: 0.7602 (m-80) REVERT: B 148 ASN cc_start: 0.6492 (p0) cc_final: 0.6286 (p0) REVERT: B 383 GLN cc_start: 0.7765 (tp40) cc_final: 0.7478 (tt0) REVERT: B 405 PHE cc_start: 0.7520 (t80) cc_final: 0.7289 (m-10) REVERT: B 591 ARG cc_start: 0.8135 (ptm160) cc_final: 0.7699 (mmt-90) REVERT: B 595 ASP cc_start: 0.7428 (m-30) cc_final: 0.6966 (t0) REVERT: B 617 ARG cc_start: 0.7719 (ttt180) cc_final: 0.7422 (ttt180) REVERT: B 632 LEU cc_start: 0.8839 (mt) cc_final: 0.8537 (mt) REVERT: B 634 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.7624 (m-80) REVERT: C 148 ASN cc_start: 0.6514 (p0) cc_final: 0.6291 (p0) REVERT: C 383 GLN cc_start: 0.7757 (tp40) cc_final: 0.7466 (tt0) REVERT: C 405 PHE cc_start: 0.7523 (t80) cc_final: 0.7289 (m-10) REVERT: C 591 ARG cc_start: 0.8136 (ptm160) cc_final: 0.7700 (mmt-90) REVERT: C 595 ASP cc_start: 0.7425 (m-30) cc_final: 0.6967 (t0) REVERT: C 617 ARG cc_start: 0.7717 (ttt180) cc_final: 0.7421 (ttt180) REVERT: C 632 LEU cc_start: 0.8835 (mt) cc_final: 0.8537 (mt) REVERT: C 634 TYR cc_start: 0.8058 (OUTLIER) cc_final: 0.7626 (m-80) REVERT: D 148 ASN cc_start: 0.6512 (p0) cc_final: 0.6307 (p0) REVERT: D 383 GLN cc_start: 0.7750 (tp40) cc_final: 0.7461 (tt0) REVERT: D 405 PHE cc_start: 0.7527 (t80) cc_final: 0.7286 (m-10) REVERT: D 591 ARG cc_start: 0.8126 (ptm160) cc_final: 0.7716 (mmt-90) REVERT: D 595 ASP cc_start: 0.7376 (m-30) cc_final: 0.7016 (t0) REVERT: D 617 ARG cc_start: 0.7725 (ttt180) cc_final: 0.7427 (ttt180) REVERT: D 632 LEU cc_start: 0.8837 (mt) cc_final: 0.8540 (mt) REVERT: D 634 TYR cc_start: 0.8071 (OUTLIER) cc_final: 0.7605 (m-80) outliers start: 16 outliers final: 4 residues processed: 367 average time/residue: 0.1863 time to fit residues: 99.1628 Evaluate side-chains 261 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 253 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 0.5980 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.5980 chunk 235 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 ASN A 154 ASN A 186 ASN A 263 ASN A 414 GLN A 487 GLN B 127 ASN B 154 ASN B 186 ASN B 263 ASN B 414 GLN B 487 GLN C 127 ASN C 154 ASN C 186 ASN C 263 ASN C 414 GLN C 487 GLN D 127 ASN D 154 ASN D 186 ASN D 263 ASN D 414 GLN D 487 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.141830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.114457 restraints weight = 26194.700| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.11 r_work: 0.3161 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20512 Z= 0.106 Angle : 0.523 5.893 27816 Z= 0.265 Chirality : 0.037 0.186 3116 Planarity : 0.006 0.076 3428 Dihedral : 8.297 59.837 2772 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.71 % Allowed : 11.72 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.15), residues: 2412 helix: -0.34 (0.12), residues: 1436 sheet: -2.91 (0.38), residues: 124 loop : -2.45 (0.17), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 539 TYR 0.011 0.001 TYR C 629 PHE 0.018 0.001 PHE B 540 TRP 0.010 0.001 TRP A 454 HIS 0.004 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00240 (20512) covalent geometry : angle 0.52315 (27816) hydrogen bonds : bond 0.03261 ( 1044) hydrogen bonds : angle 4.30709 ( 3096) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 334 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6270 (mmtm) cc_final: 0.5818 (mtmt) REVERT: A 205 THR cc_start: 0.9141 (t) cc_final: 0.8822 (m) REVERT: A 383 GLN cc_start: 0.8326 (tp40) cc_final: 0.7788 (tt0) REVERT: A 468 MET cc_start: 0.5716 (mtp) cc_final: 0.5490 (mtm) REVERT: A 469 ASP cc_start: 0.7502 (p0) cc_final: 0.7160 (p0) REVERT: A 539 ARG cc_start: 0.7663 (mtp180) cc_final: 0.7269 (mmt-90) REVERT: A 591 ARG cc_start: 0.8496 (ptm160) cc_final: 0.7658 (mmm160) REVERT: A 595 ASP cc_start: 0.8001 (m-30) cc_final: 0.7269 (t0) REVERT: A 617 ARG cc_start: 0.7620 (ttt180) cc_final: 0.7404 (ttt180) REVERT: A 634 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.7998 (m-80) REVERT: B 104 LYS cc_start: 0.6279 (mmtm) cc_final: 0.5819 (mtmt) REVERT: B 205 THR cc_start: 0.9135 (t) cc_final: 0.8816 (m) REVERT: B 383 GLN cc_start: 0.8280 (tp40) cc_final: 0.7776 (tt0) REVERT: B 469 ASP cc_start: 0.7367 (p0) cc_final: 0.7025 (p0) REVERT: B 470 SER cc_start: 0.7328 (p) cc_final: 0.7125 (m) REVERT: B 591 ARG cc_start: 0.8492 (ptm160) cc_final: 0.7670 (mmm160) REVERT: B 595 ASP cc_start: 0.8013 (m-30) cc_final: 0.7277 (t0) REVERT: B 617 ARG cc_start: 0.7601 (ttt180) cc_final: 0.7389 (ttt180) REVERT: B 634 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.7992 (m-80) REVERT: C 104 LYS cc_start: 0.6264 (mmtm) cc_final: 0.5828 (mtmt) REVERT: C 205 THR cc_start: 0.9142 (t) cc_final: 0.8820 (m) REVERT: C 383 GLN cc_start: 0.8297 (tp40) cc_final: 0.7784 (tt0) REVERT: C 469 ASP cc_start: 0.7458 (p0) cc_final: 0.7110 (p0) REVERT: C 539 ARG cc_start: 0.7653 (mtp180) cc_final: 0.7266 (mmt-90) REVERT: C 591 ARG cc_start: 0.8518 (ptm160) cc_final: 0.7676 (mmm160) REVERT: C 595 ASP cc_start: 0.8002 (m-30) cc_final: 0.7278 (t0) REVERT: C 617 ARG cc_start: 0.7631 (ttt180) cc_final: 0.7416 (ttt180) REVERT: C 634 TYR cc_start: 0.8472 (OUTLIER) cc_final: 0.8017 (m-80) REVERT: D 104 LYS cc_start: 0.6258 (mmtm) cc_final: 0.5828 (mtmt) REVERT: D 205 THR cc_start: 0.9150 (t) cc_final: 0.8834 (m) REVERT: D 383 GLN cc_start: 0.8246 (tp40) cc_final: 0.7732 (tt0) REVERT: D 468 MET cc_start: 0.5774 (mtp) cc_final: 0.5540 (mtm) REVERT: D 469 ASP cc_start: 0.7407 (p0) cc_final: 0.7078 (p0) REVERT: D 539 ARG cc_start: 0.7659 (mtp180) cc_final: 0.7266 (mmt-90) REVERT: D 591 ARG cc_start: 0.8528 (ptm160) cc_final: 0.7670 (mmm160) REVERT: D 595 ASP cc_start: 0.7994 (m-30) cc_final: 0.7262 (t0) REVERT: D 617 ARG cc_start: 0.7627 (ttt180) cc_final: 0.7422 (ttt180) REVERT: D 634 TYR cc_start: 0.8459 (OUTLIER) cc_final: 0.7993 (m-80) outliers start: 37 outliers final: 15 residues processed: 354 average time/residue: 0.1648 time to fit residues: 87.6464 Evaluate side-chains 310 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 291 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 609 GLU Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 609 GLU Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 609 GLU Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 147 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 77 optimal weight: 0.1980 chunk 177 optimal weight: 2.9990 chunk 222 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 150 optimal weight: 2.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 263 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.137358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.109418 restraints weight = 26680.004| |-----------------------------------------------------------------------------| r_work (start): 0.3221 rms_B_bonded: 2.21 r_work: 0.3091 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20512 Z= 0.172 Angle : 0.560 6.378 27816 Z= 0.277 Chirality : 0.039 0.162 3116 Planarity : 0.005 0.069 3428 Dihedral : 7.808 57.526 2772 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.91 % Allowed : 12.45 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.72 (0.16), residues: 2412 helix: 0.68 (0.13), residues: 1436 sheet: -2.39 (0.43), residues: 124 loop : -2.19 (0.18), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 539 TYR 0.014 0.001 TYR C 208 PHE 0.015 0.001 PHE B 540 TRP 0.010 0.001 TRP B 677 HIS 0.004 0.001 HIS B 251 Details of bonding type rmsd covalent geometry : bond 0.00407 (20512) covalent geometry : angle 0.56049 (27816) hydrogen bonds : bond 0.03502 ( 1044) hydrogen bonds : angle 4.06289 ( 3096) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 315 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6309 (mmtm) cc_final: 0.5722 (mtmt) REVERT: A 111 TYR cc_start: 0.8083 (m-80) cc_final: 0.7673 (m-80) REVERT: A 163 GLN cc_start: 0.7621 (tt0) cc_final: 0.7160 (tp-100) REVERT: A 205 THR cc_start: 0.9191 (t) cc_final: 0.8895 (m) REVERT: A 375 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8542 (pp) REVERT: A 539 ARG cc_start: 0.7801 (mtp180) cc_final: 0.7419 (mtt-85) REVERT: A 591 ARG cc_start: 0.8528 (ptm160) cc_final: 0.7678 (mmt-90) REVERT: A 595 ASP cc_start: 0.8173 (m-30) cc_final: 0.7360 (t0) REVERT: A 634 TYR cc_start: 0.8544 (OUTLIER) cc_final: 0.7903 (m-80) REVERT: B 104 LYS cc_start: 0.6174 (mmtm) cc_final: 0.5624 (mtmt) REVERT: B 111 TYR cc_start: 0.8051 (m-80) cc_final: 0.7692 (m-80) REVERT: B 163 GLN cc_start: 0.7616 (tt0) cc_final: 0.7165 (tp-100) REVERT: B 205 THR cc_start: 0.9184 (t) cc_final: 0.8880 (m) REVERT: B 375 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8525 (pp) REVERT: B 591 ARG cc_start: 0.8533 (ptm160) cc_final: 0.7711 (mmt-90) REVERT: B 634 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.7914 (m-80) REVERT: C 104 LYS cc_start: 0.6239 (mmtm) cc_final: 0.5668 (mtmt) REVERT: C 111 TYR cc_start: 0.8081 (m-80) cc_final: 0.7684 (m-80) REVERT: C 163 GLN cc_start: 0.7652 (tt0) cc_final: 0.7197 (tp-100) REVERT: C 205 THR cc_start: 0.9188 (t) cc_final: 0.8887 (m) REVERT: C 375 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8533 (pp) REVERT: C 539 ARG cc_start: 0.7925 (mtp180) cc_final: 0.7526 (mtt-85) REVERT: C 591 ARG cc_start: 0.8501 (ptm160) cc_final: 0.7709 (mmt-90) REVERT: C 617 ARG cc_start: 0.7666 (ttt180) cc_final: 0.7433 (ttt180) REVERT: C 634 TYR cc_start: 0.8526 (OUTLIER) cc_final: 0.7882 (m-80) REVERT: D 104 LYS cc_start: 0.6170 (mmtm) cc_final: 0.5620 (mtmt) REVERT: D 111 TYR cc_start: 0.8065 (m-80) cc_final: 0.7665 (m-80) REVERT: D 163 GLN cc_start: 0.7649 (tt0) cc_final: 0.7199 (tp-100) REVERT: D 205 THR cc_start: 0.9199 (t) cc_final: 0.8898 (m) REVERT: D 375 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8497 (pp) REVERT: D 539 ARG cc_start: 0.7924 (mtp180) cc_final: 0.7531 (mtt-85) REVERT: D 591 ARG cc_start: 0.8508 (ptm160) cc_final: 0.7687 (mmt-90) REVERT: D 595 ASP cc_start: 0.8139 (m-30) cc_final: 0.7343 (t0) REVERT: D 617 ARG cc_start: 0.7647 (ttt180) cc_final: 0.7428 (ttt180) REVERT: D 634 TYR cc_start: 0.8546 (OUTLIER) cc_final: 0.7909 (m-80) outliers start: 63 outliers final: 48 residues processed: 361 average time/residue: 0.1604 time to fit residues: 87.7595 Evaluate side-chains 339 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 283 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 391 SER Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 391 SER Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 610 LEU Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 610 LEU Chi-restraints excluded: chain D residue 621 VAL Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 160 optimal weight: 0.0670 chunk 158 optimal weight: 0.9990 chunk 215 optimal weight: 0.7980 chunk 214 optimal weight: 1.9990 chunk 87 optimal weight: 0.1980 chunk 44 optimal weight: 0.8980 chunk 5 optimal weight: 0.0770 chunk 139 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 overall best weight: 0.3876 ------------------------------------------------------------------------------- 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 = 0.3645 r_free = 0.3645 target = 0.142647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.115178 restraints weight = 26405.790| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.21 r_work: 0.3167 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 20512 Z= 0.087 Angle : 0.487 5.727 27816 Z= 0.242 Chirality : 0.036 0.132 3116 Planarity : 0.004 0.060 3428 Dihedral : 7.516 59.868 2772 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.75 % Allowed : 14.94 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.17), residues: 2412 helix: 1.32 (0.14), residues: 1444 sheet: -2.24 (0.44), residues: 116 loop : -1.96 (0.19), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 388 TYR 0.008 0.001 TYR B 105 PHE 0.011 0.001 PHE B 540 TRP 0.008 0.001 TRP A 454 HIS 0.003 0.001 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00192 (20512) covalent geometry : angle 0.48694 (27816) hydrogen bonds : bond 0.02817 ( 1044) hydrogen bonds : angle 3.70782 ( 3096) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 339 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6204 (mmtm) cc_final: 0.5718 (mtmt) REVERT: A 111 TYR cc_start: 0.8059 (m-80) cc_final: 0.7574 (m-80) REVERT: A 135 CYS cc_start: 0.8616 (t) cc_final: 0.7892 (p) REVERT: A 163 GLN cc_start: 0.7431 (tt0) cc_final: 0.7009 (tp-100) REVERT: A 173 GLU cc_start: 0.8369 (tp30) cc_final: 0.7974 (tp30) REVERT: A 205 THR cc_start: 0.9185 (t) cc_final: 0.8870 (m) REVERT: A 375 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8515 (pp) REVERT: A 539 ARG cc_start: 0.7956 (mtp180) cc_final: 0.7613 (mtt-85) REVERT: A 591 ARG cc_start: 0.8427 (ptm160) cc_final: 0.7633 (mmm160) REVERT: A 634 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7843 (m-80) REVERT: A 640 MET cc_start: 0.8407 (tmm) cc_final: 0.8064 (ttp) REVERT: B 104 LYS cc_start: 0.6052 (mmtm) cc_final: 0.5588 (mtmt) REVERT: B 111 TYR cc_start: 0.7958 (m-80) cc_final: 0.7516 (m-80) REVERT: B 135 CYS cc_start: 0.8593 (t) cc_final: 0.7926 (p) REVERT: B 163 GLN cc_start: 0.7492 (tt0) cc_final: 0.7096 (tp-100) REVERT: B 173 GLU cc_start: 0.8372 (tp30) cc_final: 0.7986 (tp30) REVERT: B 205 THR cc_start: 0.9185 (t) cc_final: 0.8868 (m) REVERT: B 375 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8507 (pp) REVERT: B 405 PHE cc_start: 0.7761 (t80) cc_final: 0.7407 (m-10) REVERT: B 591 ARG cc_start: 0.8452 (ptm160) cc_final: 0.7646 (mmm160) REVERT: B 634 TYR cc_start: 0.8471 (OUTLIER) cc_final: 0.7842 (m-80) REVERT: B 640 MET cc_start: 0.8467 (tmm) cc_final: 0.7929 (ttp) REVERT: C 104 LYS cc_start: 0.6055 (mmtm) cc_final: 0.5591 (mtmt) REVERT: C 111 TYR cc_start: 0.8035 (m-80) cc_final: 0.7560 (m-80) REVERT: C 135 CYS cc_start: 0.8581 (t) cc_final: 0.7916 (p) REVERT: C 163 GLN cc_start: 0.7444 (tt0) cc_final: 0.7015 (tp-100) REVERT: C 173 GLU cc_start: 0.8390 (tp30) cc_final: 0.8004 (tp30) REVERT: C 205 THR cc_start: 0.9198 (t) cc_final: 0.8874 (m) REVERT: C 375 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8523 (pp) REVERT: C 405 PHE cc_start: 0.7754 (t80) cc_final: 0.7430 (m-10) REVERT: C 539 ARG cc_start: 0.7955 (mtp180) cc_final: 0.7608 (mtt-85) REVERT: C 591 ARG cc_start: 0.8456 (ptm160) cc_final: 0.7654 (mmm160) REVERT: C 634 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.7848 (m-80) REVERT: C 640 MET cc_start: 0.8412 (tmm) cc_final: 0.8064 (ttp) REVERT: D 104 LYS cc_start: 0.6044 (mmtm) cc_final: 0.5575 (mtmt) REVERT: D 111 TYR cc_start: 0.8053 (m-80) cc_final: 0.7572 (m-80) REVERT: D 135 CYS cc_start: 0.8587 (t) cc_final: 0.7923 (p) REVERT: D 163 GLN cc_start: 0.7442 (tt0) cc_final: 0.7010 (tp-100) REVERT: D 173 GLU cc_start: 0.8352 (tp30) cc_final: 0.7958 (tp30) REVERT: D 205 THR cc_start: 0.9195 (t) cc_final: 0.8884 (m) REVERT: D 375 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8432 (pp) REVERT: D 405 PHE cc_start: 0.7764 (t80) cc_final: 0.7425 (m-10) REVERT: D 539 ARG cc_start: 0.7951 (mtp180) cc_final: 0.7607 (mtt-85) REVERT: D 591 ARG cc_start: 0.8448 (ptm160) cc_final: 0.7643 (mmm160) REVERT: D 634 TYR cc_start: 0.8478 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: D 640 MET cc_start: 0.8423 (tmm) cc_final: 0.8081 (ttp) outliers start: 38 outliers final: 22 residues processed: 365 average time/residue: 0.1600 time to fit residues: 89.7182 Evaluate side-chains 331 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 301 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 159 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 101 optimal weight: 0.1980 chunk 75 optimal weight: 3.9990 chunk 133 optimal weight: 0.4980 chunk 65 optimal weight: 0.0170 chunk 97 optimal weight: 3.9990 chunk 39 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 61 optimal weight: 10.0000 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 683 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.142182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.115279 restraints weight = 26441.770| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.11 r_work: 0.3172 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 20512 Z= 0.098 Angle : 0.491 6.424 27816 Z= 0.243 Chirality : 0.036 0.120 3116 Planarity : 0.004 0.056 3428 Dihedral : 7.098 57.636 2772 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.17 % Allowed : 15.22 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.17), residues: 2412 helix: 1.70 (0.14), residues: 1444 sheet: -1.91 (0.45), residues: 124 loop : -1.68 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 388 TYR 0.023 0.001 TYR A 447 PHE 0.009 0.001 PHE B 540 TRP 0.007 0.001 TRP A 454 HIS 0.003 0.001 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00225 (20512) covalent geometry : angle 0.49056 (27816) hydrogen bonds : bond 0.02858 ( 1044) hydrogen bonds : angle 3.61047 ( 3096) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 325 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6219 (mmtm) cc_final: 0.5738 (mtmt) REVERT: A 111 TYR cc_start: 0.8046 (m-80) cc_final: 0.7682 (m-80) REVERT: A 163 GLN cc_start: 0.7592 (tt0) cc_final: 0.7135 (tp-100) REVERT: A 173 GLU cc_start: 0.8403 (tp30) cc_final: 0.8141 (tp30) REVERT: A 205 THR cc_start: 0.9206 (t) cc_final: 0.8902 (m) REVERT: A 277 MET cc_start: 0.8942 (tpp) cc_final: 0.8443 (mmt) REVERT: A 345 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8396 (mt) REVERT: A 375 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8476 (pp) REVERT: A 383 GLN cc_start: 0.8343 (tp-100) cc_final: 0.7764 (tm-30) REVERT: A 539 ARG cc_start: 0.7955 (mtp180) cc_final: 0.7632 (mtt-85) REVERT: A 591 ARG cc_start: 0.8408 (ptm160) cc_final: 0.7669 (mmt-90) REVERT: A 634 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.7789 (m-80) REVERT: A 640 MET cc_start: 0.8435 (tmm) cc_final: 0.8053 (ttp) REVERT: A 655 ASN cc_start: 0.8290 (m-40) cc_final: 0.8038 (t0) REVERT: B 104 LYS cc_start: 0.6069 (mmtm) cc_final: 0.5677 (mtmt) REVERT: B 111 TYR cc_start: 0.7984 (m-80) cc_final: 0.7593 (m-80) REVERT: B 135 CYS cc_start: 0.8577 (t) cc_final: 0.7853 (p) REVERT: B 163 GLN cc_start: 0.7593 (tt0) cc_final: 0.7125 (tp-100) REVERT: B 205 THR cc_start: 0.9199 (t) cc_final: 0.8888 (m) REVERT: B 277 MET cc_start: 0.8935 (tpp) cc_final: 0.8469 (mmt) REVERT: B 345 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8417 (mt) REVERT: B 375 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8473 (pp) REVERT: B 383 GLN cc_start: 0.8333 (tp-100) cc_final: 0.7747 (tm-30) REVERT: B 405 PHE cc_start: 0.7763 (t80) cc_final: 0.7445 (m-10) REVERT: B 496 TRP cc_start: 0.8152 (m100) cc_final: 0.7704 (m100) REVERT: B 591 ARG cc_start: 0.8446 (ptm160) cc_final: 0.7661 (mmm160) REVERT: B 634 TYR cc_start: 0.8480 (OUTLIER) cc_final: 0.7860 (m-80) REVERT: B 640 MET cc_start: 0.8478 (tmm) cc_final: 0.8080 (ttp) REVERT: B 655 ASN cc_start: 0.8280 (m-40) cc_final: 0.8016 (t0) REVERT: C 104 LYS cc_start: 0.6079 (mmtm) cc_final: 0.5634 (mtmt) REVERT: C 111 TYR cc_start: 0.8064 (m-80) cc_final: 0.7635 (m-80) REVERT: C 135 CYS cc_start: 0.8492 (t) cc_final: 0.7755 (p) REVERT: C 163 GLN cc_start: 0.7599 (tt0) cc_final: 0.7125 (tp-100) REVERT: C 205 THR cc_start: 0.9206 (t) cc_final: 0.8892 (m) REVERT: C 277 MET cc_start: 0.8971 (tpp) cc_final: 0.8480 (mmt) REVERT: C 345 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8405 (mt) REVERT: C 375 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8490 (pp) REVERT: C 383 GLN cc_start: 0.8400 (tp-100) cc_final: 0.7827 (tm-30) REVERT: C 405 PHE cc_start: 0.7767 (t80) cc_final: 0.7469 (m-10) REVERT: C 539 ARG cc_start: 0.7947 (mtp180) cc_final: 0.7622 (mtt-85) REVERT: C 591 ARG cc_start: 0.8432 (ptm160) cc_final: 0.7659 (mmm160) REVERT: C 634 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7814 (m-80) REVERT: C 640 MET cc_start: 0.8438 (tmm) cc_final: 0.8033 (ttp) REVERT: C 645 MET cc_start: 0.7821 (tpp) cc_final: 0.7550 (tpp) REVERT: C 655 ASN cc_start: 0.8313 (m-40) cc_final: 0.8046 (t0) REVERT: D 104 LYS cc_start: 0.6067 (mmtm) cc_final: 0.5663 (mtmt) REVERT: D 111 TYR cc_start: 0.8068 (m-80) cc_final: 0.7625 (m-80) REVERT: D 135 CYS cc_start: 0.8480 (t) cc_final: 0.7746 (p) REVERT: D 163 GLN cc_start: 0.7606 (tt0) cc_final: 0.7150 (tp-100) REVERT: D 205 THR cc_start: 0.9208 (t) cc_final: 0.8897 (m) REVERT: D 277 MET cc_start: 0.8959 (tpp) cc_final: 0.8464 (mmt) REVERT: D 345 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8398 (mt) REVERT: D 375 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8437 (pp) REVERT: D 405 PHE cc_start: 0.7782 (t80) cc_final: 0.7468 (m-10) REVERT: D 539 ARG cc_start: 0.7956 (mtp180) cc_final: 0.7632 (mtt-85) REVERT: D 591 ARG cc_start: 0.8425 (ptm160) cc_final: 0.7651 (mmm160) REVERT: D 634 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.7804 (m-80) REVERT: D 640 MET cc_start: 0.8463 (tmm) cc_final: 0.8068 (ttp) REVERT: D 655 ASN cc_start: 0.8329 (m-40) cc_final: 0.8070 (t0) outliers start: 47 outliers final: 31 residues processed: 360 average time/residue: 0.1561 time to fit residues: 85.8813 Evaluate side-chains 348 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 305 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 621 VAL Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 207 optimal weight: 1.9990 chunk 65 optimal weight: 0.0470 chunk 173 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 169 optimal weight: 7.9990 chunk 142 optimal weight: 0.4980 chunk 74 optimal weight: 0.3980 chunk 150 optimal weight: 0.6980 chunk 126 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.143457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.116698 restraints weight = 26232.784| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.10 r_work: 0.3188 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 20512 Z= 0.088 Angle : 0.479 6.216 27816 Z= 0.238 Chirality : 0.036 0.118 3116 Planarity : 0.004 0.053 3428 Dihedral : 6.555 53.615 2772 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.58 % Allowed : 15.64 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.17), residues: 2412 helix: 1.94 (0.14), residues: 1444 sheet: -1.88 (0.45), residues: 116 loop : -1.54 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 388 TYR 0.019 0.001 TYR A 447 PHE 0.008 0.001 PHE B 540 TRP 0.006 0.001 TRP A 454 HIS 0.003 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00202 (20512) covalent geometry : angle 0.47900 (27816) hydrogen bonds : bond 0.02713 ( 1044) hydrogen bonds : angle 3.49860 ( 3096) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 330 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6127 (mmtm) cc_final: 0.5709 (mtmt) REVERT: A 111 TYR cc_start: 0.8069 (m-80) cc_final: 0.7746 (m-80) REVERT: A 163 GLN cc_start: 0.7519 (tt0) cc_final: 0.7054 (tp40) REVERT: A 205 THR cc_start: 0.9140 (t) cc_final: 0.8839 (m) REVERT: A 277 MET cc_start: 0.8880 (tpp) cc_final: 0.8399 (mmt) REVERT: A 345 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8400 (mt) REVERT: A 375 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8452 (pp) REVERT: A 383 GLN cc_start: 0.8275 (tp-100) cc_final: 0.7667 (tm-30) REVERT: A 539 ARG cc_start: 0.7912 (mtp180) cc_final: 0.7536 (mtt90) REVERT: A 591 ARG cc_start: 0.8405 (ptm160) cc_final: 0.7624 (mmm160) REVERT: A 634 TYR cc_start: 0.8432 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: A 640 MET cc_start: 0.8392 (tmm) cc_final: 0.8053 (ttp) REVERT: A 655 ASN cc_start: 0.8252 (m-40) cc_final: 0.8036 (t0) REVERT: B 104 LYS cc_start: 0.6067 (mmtm) cc_final: 0.5652 (mtmt) REVERT: B 111 TYR cc_start: 0.7962 (m-80) cc_final: 0.7651 (m-80) REVERT: B 135 CYS cc_start: 0.8454 (t) cc_final: 0.7680 (p) REVERT: B 163 GLN cc_start: 0.7534 (tt0) cc_final: 0.7005 (tp40) REVERT: B 205 THR cc_start: 0.9133 (t) cc_final: 0.8826 (m) REVERT: B 277 MET cc_start: 0.8896 (tpp) cc_final: 0.8421 (mmt) REVERT: B 375 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8477 (pp) REVERT: B 383 GLN cc_start: 0.8255 (tp-100) cc_final: 0.7647 (tm-30) REVERT: B 405 PHE cc_start: 0.7702 (t80) cc_final: 0.7378 (m-10) REVERT: B 591 ARG cc_start: 0.8407 (ptm160) cc_final: 0.7678 (mmt-90) REVERT: B 634 TYR cc_start: 0.8443 (OUTLIER) cc_final: 0.7800 (m-80) REVERT: B 640 MET cc_start: 0.8400 (tmm) cc_final: 0.8071 (ttp) REVERT: B 655 ASN cc_start: 0.8243 (m-40) cc_final: 0.8016 (t0) REVERT: C 104 LYS cc_start: 0.6069 (mmtm) cc_final: 0.5651 (mtmt) REVERT: C 111 TYR cc_start: 0.8012 (m-80) cc_final: 0.7640 (m-80) REVERT: C 135 CYS cc_start: 0.8476 (t) cc_final: 0.7680 (p) REVERT: C 163 GLN cc_start: 0.7533 (tt0) cc_final: 0.7069 (tp40) REVERT: C 205 THR cc_start: 0.9139 (t) cc_final: 0.8830 (m) REVERT: C 277 MET cc_start: 0.8907 (tpp) cc_final: 0.8431 (mmt) REVERT: C 375 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8492 (pp) REVERT: C 383 GLN cc_start: 0.8283 (tp-100) cc_final: 0.7685 (tm-30) REVERT: C 405 PHE cc_start: 0.7692 (t80) cc_final: 0.7378 (m-10) REVERT: C 539 ARG cc_start: 0.7895 (mtp180) cc_final: 0.7576 (mtt-85) REVERT: C 591 ARG cc_start: 0.8406 (ptm160) cc_final: 0.7651 (mmm160) REVERT: C 634 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: C 640 MET cc_start: 0.8418 (tmm) cc_final: 0.8089 (ttp) REVERT: C 655 ASN cc_start: 0.8276 (m-40) cc_final: 0.8052 (t0) REVERT: D 104 LYS cc_start: 0.6000 (mmtm) cc_final: 0.5522 (mtmt) REVERT: D 111 TYR cc_start: 0.8035 (m-80) cc_final: 0.7718 (m-80) REVERT: D 135 CYS cc_start: 0.8452 (t) cc_final: 0.7678 (p) REVERT: D 163 GLN cc_start: 0.7536 (tt0) cc_final: 0.7045 (tp40) REVERT: D 205 THR cc_start: 0.9134 (t) cc_final: 0.8831 (m) REVERT: D 277 MET cc_start: 0.8899 (tpp) cc_final: 0.8430 (mmt) REVERT: D 375 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8411 (pp) REVERT: D 383 GLN cc_start: 0.8272 (tp-100) cc_final: 0.7677 (tm-30) REVERT: D 405 PHE cc_start: 0.7706 (t80) cc_final: 0.7382 (m-10) REVERT: D 539 ARG cc_start: 0.7915 (mtp180) cc_final: 0.7595 (mtt-85) REVERT: D 591 ARG cc_start: 0.8414 (ptm160) cc_final: 0.7664 (mmt-90) REVERT: D 634 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.7799 (m-80) REVERT: D 640 MET cc_start: 0.8428 (tmm) cc_final: 0.8090 (ttp) REVERT: D 655 ASN cc_start: 0.8273 (m-40) cc_final: 0.8053 (t0) outliers start: 56 outliers final: 28 residues processed: 375 average time/residue: 0.1532 time to fit residues: 88.2962 Evaluate side-chains 342 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 305 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 634 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 49 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 215 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 61 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 238 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 316 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.138309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.111128 restraints weight = 26667.613| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.10 r_work: 0.3115 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20512 Z= 0.172 Angle : 0.564 7.886 27816 Z= 0.278 Chirality : 0.039 0.152 3116 Planarity : 0.004 0.057 3428 Dihedral : 6.863 55.612 2772 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.12 % Allowed : 16.19 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.17), residues: 2412 helix: 1.79 (0.13), residues: 1436 sheet: -1.91 (0.46), residues: 116 loop : -1.52 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 539 TYR 0.016 0.001 TYR A 447 PHE 0.011 0.001 PHE B 549 TRP 0.008 0.001 TRP D 454 HIS 0.004 0.001 HIS A 251 Details of bonding type rmsd covalent geometry : bond 0.00414 (20512) covalent geometry : angle 0.56432 (27816) hydrogen bonds : bond 0.03282 ( 1044) hydrogen bonds : angle 3.73632 ( 3096) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 288 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6195 (mmtm) cc_final: 0.5726 (mtmt) REVERT: A 111 TYR cc_start: 0.8077 (m-80) cc_final: 0.7752 (m-80) REVERT: A 163 GLN cc_start: 0.7717 (tt0) cc_final: 0.7227 (tp40) REVERT: A 173 GLU cc_start: 0.8346 (tp30) cc_final: 0.8035 (tp30) REVERT: A 205 THR cc_start: 0.9204 (t) cc_final: 0.8890 (m) REVERT: A 345 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8644 (mt) REVERT: A 375 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8571 (pp) REVERT: A 383 GLN cc_start: 0.8450 (tp-100) cc_final: 0.7830 (tm-30) REVERT: A 539 ARG cc_start: 0.7969 (mtp180) cc_final: 0.7623 (mtt-85) REVERT: A 591 ARG cc_start: 0.8447 (ptm160) cc_final: 0.7732 (mmt-90) REVERT: A 634 TYR cc_start: 0.8508 (OUTLIER) cc_final: 0.7884 (m-80) REVERT: B 104 LYS cc_start: 0.6153 (mmtm) cc_final: 0.5717 (mtmt) REVERT: B 111 TYR cc_start: 0.8017 (m-80) cc_final: 0.7698 (m-80) REVERT: B 163 GLN cc_start: 0.7736 (tt0) cc_final: 0.7240 (tp40) REVERT: B 205 THR cc_start: 0.9192 (t) cc_final: 0.8878 (m) REVERT: B 375 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8602 (pp) REVERT: B 383 GLN cc_start: 0.8430 (tp-100) cc_final: 0.7834 (tm-30) REVERT: B 405 PHE cc_start: 0.7689 (t80) cc_final: 0.7431 (m-10) REVERT: B 591 ARG cc_start: 0.8495 (ptm160) cc_final: 0.7719 (mmt-90) REVERT: B 634 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.7899 (m-80) REVERT: C 104 LYS cc_start: 0.6163 (mmtm) cc_final: 0.5731 (mtmt) REVERT: C 111 TYR cc_start: 0.8076 (m-80) cc_final: 0.7705 (m-80) REVERT: C 163 GLN cc_start: 0.7730 (tt0) cc_final: 0.7242 (tp40) REVERT: C 205 THR cc_start: 0.9192 (t) cc_final: 0.8869 (m) REVERT: C 375 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8583 (pp) REVERT: C 383 GLN cc_start: 0.8474 (tp-100) cc_final: 0.7862 (tm-30) REVERT: C 405 PHE cc_start: 0.7679 (t80) cc_final: 0.7439 (m-10) REVERT: C 539 ARG cc_start: 0.7980 (mtp180) cc_final: 0.7624 (mtt-85) REVERT: C 591 ARG cc_start: 0.8469 (ptm160) cc_final: 0.7707 (mmt-90) REVERT: C 634 TYR cc_start: 0.8505 (OUTLIER) cc_final: 0.7890 (m-80) REVERT: C 645 MET cc_start: 0.7907 (tpp) cc_final: 0.7688 (tpp) REVERT: D 104 LYS cc_start: 0.6105 (mmtm) cc_final: 0.5764 (mtmt) REVERT: D 111 TYR cc_start: 0.8064 (m-80) cc_final: 0.7708 (m-80) REVERT: D 163 GLN cc_start: 0.7705 (tt0) cc_final: 0.7120 (tp40) REVERT: D 205 THR cc_start: 0.9189 (t) cc_final: 0.8873 (m) REVERT: D 375 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8552 (pp) REVERT: D 383 GLN cc_start: 0.8464 (tp-100) cc_final: 0.7847 (tm-30) REVERT: D 405 PHE cc_start: 0.7684 (t80) cc_final: 0.7435 (m-10) REVERT: D 539 ARG cc_start: 0.7994 (mtp180) cc_final: 0.7643 (mtt-85) REVERT: D 591 ARG cc_start: 0.8457 (ptm160) cc_final: 0.7705 (mmt-90) REVERT: D 634 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.7874 (m-80) outliers start: 46 outliers final: 36 residues processed: 325 average time/residue: 0.1586 time to fit residues: 79.3740 Evaluate side-chains 326 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 281 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 656 SER Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 656 SER Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 656 SER Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 9 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 195 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 153 optimal weight: 0.7980 chunk 236 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3617 r_free = 0.3617 target = 0.140318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.113332 restraints weight = 26528.338| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.10 r_work: 0.3140 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20512 Z= 0.120 Angle : 0.528 6.267 27816 Z= 0.261 Chirality : 0.037 0.141 3116 Planarity : 0.004 0.056 3428 Dihedral : 6.882 55.326 2772 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.26 % Allowed : 16.47 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.17), residues: 2412 helix: 1.87 (0.13), residues: 1436 sheet: -1.76 (0.45), residues: 124 loop : -1.37 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 539 TYR 0.016 0.001 TYR A 447 PHE 0.008 0.001 PHE B 540 TRP 0.007 0.001 TRP A 677 HIS 0.003 0.001 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00285 (20512) covalent geometry : angle 0.52843 (27816) hydrogen bonds : bond 0.03042 ( 1044) hydrogen bonds : angle 3.65269 ( 3096) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 297 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6207 (mmtm) cc_final: 0.5680 (mtmt) REVERT: A 111 TYR cc_start: 0.8092 (m-80) cc_final: 0.7760 (m-80) REVERT: A 163 GLN cc_start: 0.7576 (tt0) cc_final: 0.7074 (tp40) REVERT: A 173 GLU cc_start: 0.8277 (tp30) cc_final: 0.8002 (tp30) REVERT: A 277 MET cc_start: 0.8896 (tpp) cc_final: 0.8381 (mmt) REVERT: A 345 LEU cc_start: 0.8796 (pp) cc_final: 0.8539 (mt) REVERT: A 375 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8585 (pp) REVERT: A 383 GLN cc_start: 0.8394 (tp-100) cc_final: 0.7775 (tm-30) REVERT: A 591 ARG cc_start: 0.8369 (ptm160) cc_final: 0.7653 (mmm160) REVERT: A 634 TYR cc_start: 0.8492 (OUTLIER) cc_final: 0.7863 (m-80) REVERT: B 104 LYS cc_start: 0.6120 (mmtm) cc_final: 0.5692 (mtmt) REVERT: B 111 TYR cc_start: 0.7946 (m-80) cc_final: 0.7646 (m-80) REVERT: B 163 GLN cc_start: 0.7565 (tt0) cc_final: 0.7057 (tp40) REVERT: B 173 GLU cc_start: 0.8352 (tp30) cc_final: 0.7979 (tp30) REVERT: B 277 MET cc_start: 0.8919 (tpp) cc_final: 0.8374 (mmt) REVERT: B 375 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8597 (pp) REVERT: B 383 GLN cc_start: 0.8373 (tp-100) cc_final: 0.7763 (tm-30) REVERT: B 405 PHE cc_start: 0.7754 (t80) cc_final: 0.7382 (m-10) REVERT: B 591 ARG cc_start: 0.8414 (ptm160) cc_final: 0.7662 (mmm160) REVERT: B 634 TYR cc_start: 0.8497 (OUTLIER) cc_final: 0.7870 (m-80) REVERT: B 645 MET cc_start: 0.7459 (tpp) cc_final: 0.7218 (tpp) REVERT: C 104 LYS cc_start: 0.6125 (mmtm) cc_final: 0.5753 (mtmt) REVERT: C 111 TYR cc_start: 0.8038 (m-80) cc_final: 0.7674 (m-80) REVERT: C 163 GLN cc_start: 0.7641 (tt0) cc_final: 0.7142 (tp40) REVERT: C 173 GLU cc_start: 0.8357 (tp30) cc_final: 0.7984 (tp30) REVERT: C 277 MET cc_start: 0.8925 (tpp) cc_final: 0.8423 (mmt) REVERT: C 375 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8600 (pp) REVERT: C 383 GLN cc_start: 0.8399 (tp-100) cc_final: 0.7785 (tm-30) REVERT: C 405 PHE cc_start: 0.7738 (t80) cc_final: 0.7394 (m-10) REVERT: C 591 ARG cc_start: 0.8411 (ptm160) cc_final: 0.7654 (mmm160) REVERT: C 634 TYR cc_start: 0.8493 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: C 645 MET cc_start: 0.7851 (tpp) cc_final: 0.7467 (tpp) REVERT: D 104 LYS cc_start: 0.6148 (mmtm) cc_final: 0.5702 (mtmt) REVERT: D 111 TYR cc_start: 0.8048 (m-80) cc_final: 0.7733 (m-80) REVERT: D 163 GLN cc_start: 0.7543 (tt0) cc_final: 0.7046 (tp40) REVERT: D 277 MET cc_start: 0.8916 (tpp) cc_final: 0.8420 (mmt) REVERT: D 375 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8550 (pp) REVERT: D 383 GLN cc_start: 0.8405 (tp-100) cc_final: 0.7761 (tm-30) REVERT: D 405 PHE cc_start: 0.7749 (t80) cc_final: 0.7398 (m-10) REVERT: D 591 ARG cc_start: 0.8419 (ptm160) cc_final: 0.7649 (mmm160) REVERT: D 634 TYR cc_start: 0.8489 (OUTLIER) cc_final: 0.7860 (m-80) outliers start: 49 outliers final: 34 residues processed: 338 average time/residue: 0.1499 time to fit residues: 78.0529 Evaluate side-chains 332 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 290 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 621 VAL Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 111 optimal weight: 0.3980 chunk 235 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 3 optimal weight: 9.9990 chunk 231 optimal weight: 0.7980 chunk 54 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 639 ASN C 639 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.140772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.114183 restraints weight = 26401.732| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.07 r_work: 0.3156 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 20512 Z= 0.110 Angle : 0.524 7.957 27816 Z= 0.260 Chirality : 0.038 0.195 3116 Planarity : 0.004 0.056 3428 Dihedral : 6.844 52.891 2772 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.89 % Allowed : 17.02 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.17), residues: 2412 helix: 1.95 (0.13), residues: 1436 sheet: -1.66 (0.45), residues: 124 loop : -1.30 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 539 TYR 0.033 0.001 TYR A 98 PHE 0.008 0.001 PHE B 540 TRP 0.007 0.001 TRP A 677 HIS 0.003 0.001 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00260 (20512) covalent geometry : angle 0.52419 (27816) hydrogen bonds : bond 0.02956 ( 1044) hydrogen bonds : angle 3.63260 ( 3096) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 301 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6330 (mmtm) cc_final: 0.5807 (mtmt) REVERT: A 111 TYR cc_start: 0.8068 (m-80) cc_final: 0.7756 (m-80) REVERT: A 163 GLN cc_start: 0.7582 (tt0) cc_final: 0.7002 (tp40) REVERT: A 173 GLU cc_start: 0.8297 (tp30) cc_final: 0.8046 (tp30) REVERT: A 205 THR cc_start: 0.9072 (t) cc_final: 0.8721 (m) REVERT: A 277 MET cc_start: 0.8893 (tpp) cc_final: 0.8342 (mmt) REVERT: A 345 LEU cc_start: 0.8772 (pp) cc_final: 0.8552 (mt) REVERT: A 375 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8595 (pp) REVERT: A 383 GLN cc_start: 0.8400 (tp-100) cc_final: 0.7810 (tm-30) REVERT: A 591 ARG cc_start: 0.8389 (ptm160) cc_final: 0.7635 (mmm160) REVERT: A 634 TYR cc_start: 0.8491 (OUTLIER) cc_final: 0.7844 (m-80) REVERT: B 104 LYS cc_start: 0.6163 (mmtm) cc_final: 0.5673 (mtmt) REVERT: B 111 TYR cc_start: 0.7933 (m-80) cc_final: 0.7681 (m-80) REVERT: B 163 GLN cc_start: 0.7648 (tt0) cc_final: 0.7119 (tp40) REVERT: B 173 GLU cc_start: 0.8354 (tp30) cc_final: 0.8013 (tp30) REVERT: B 205 THR cc_start: 0.9069 (t) cc_final: 0.8706 (m) REVERT: B 277 MET cc_start: 0.8876 (tpp) cc_final: 0.8338 (mmt) REVERT: B 375 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8635 (pp) REVERT: B 383 GLN cc_start: 0.8360 (tp-100) cc_final: 0.7786 (tm-30) REVERT: B 405 PHE cc_start: 0.7784 (t80) cc_final: 0.7460 (m-10) REVERT: B 591 ARG cc_start: 0.8412 (ptm160) cc_final: 0.7641 (mmm160) REVERT: B 634 TYR cc_start: 0.8535 (OUTLIER) cc_final: 0.7916 (m-80) REVERT: C 104 LYS cc_start: 0.6217 (mmtm) cc_final: 0.5710 (mtmt) REVERT: C 111 TYR cc_start: 0.8059 (m-80) cc_final: 0.7728 (m-80) REVERT: C 163 GLN cc_start: 0.7597 (tt0) cc_final: 0.6991 (tp40) REVERT: C 173 GLU cc_start: 0.8415 (tp30) cc_final: 0.8073 (tp30) REVERT: C 205 THR cc_start: 0.9081 (t) cc_final: 0.8732 (m) REVERT: C 277 MET cc_start: 0.8882 (tpp) cc_final: 0.8334 (mmt) REVERT: C 375 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8598 (pp) REVERT: C 383 GLN cc_start: 0.8404 (tp-100) cc_final: 0.7811 (tm-30) REVERT: C 405 PHE cc_start: 0.7649 (t80) cc_final: 0.7439 (m-10) REVERT: C 539 ARG cc_start: 0.7975 (mtp180) cc_final: 0.7653 (mtt-85) REVERT: C 591 ARG cc_start: 0.8383 (ptm160) cc_final: 0.7637 (mmm160) REVERT: C 634 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.7835 (m-80) REVERT: C 640 MET cc_start: 0.8401 (tmm) cc_final: 0.7933 (ttp) REVERT: C 645 MET cc_start: 0.7882 (tpp) cc_final: 0.7529 (tpp) REVERT: D 104 LYS cc_start: 0.6138 (mmtm) cc_final: 0.5720 (mtmt) REVERT: D 111 TYR cc_start: 0.8054 (m-80) cc_final: 0.7779 (m-80) REVERT: D 163 GLN cc_start: 0.7593 (tt0) cc_final: 0.7077 (tp40) REVERT: D 173 GLU cc_start: 0.8380 (tp30) cc_final: 0.7904 (tp30) REVERT: D 205 THR cc_start: 0.9075 (t) cc_final: 0.8721 (m) REVERT: D 277 MET cc_start: 0.8869 (tpp) cc_final: 0.8338 (mmt) REVERT: D 375 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8595 (pp) REVERT: D 383 GLN cc_start: 0.8415 (tp-100) cc_final: 0.7833 (tm-30) REVERT: D 405 PHE cc_start: 0.7779 (t80) cc_final: 0.7468 (m-10) REVERT: D 539 ARG cc_start: 0.7925 (mtp180) cc_final: 0.7646 (mtt-85) REVERT: D 591 ARG cc_start: 0.8434 (ptm160) cc_final: 0.7647 (mmm160) REVERT: D 634 TYR cc_start: 0.8536 (OUTLIER) cc_final: 0.7914 (m-80) outliers start: 41 outliers final: 33 residues processed: 334 average time/residue: 0.1437 time to fit residues: 73.1027 Evaluate side-chains 341 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 300 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 621 VAL Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 127 optimal weight: 0.9980 chunk 24 optimal weight: 0.0570 chunk 97 optimal weight: 0.9980 chunk 174 optimal weight: 0.8980 chunk 206 optimal weight: 1.9990 chunk 108 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 chunk 192 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.9900 ------------------------------------------------------------------------------- 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 = 0.3620 r_free = 0.3620 target = 0.140026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.113437 restraints weight = 26397.038| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.06 r_work: 0.3161 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20512 Z= 0.115 Angle : 0.528 9.570 27816 Z= 0.262 Chirality : 0.038 0.179 3116 Planarity : 0.004 0.055 3428 Dihedral : 6.780 52.960 2772 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.12 % Allowed : 16.88 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.17), residues: 2412 helix: 2.01 (0.13), residues: 1436 sheet: -1.64 (0.46), residues: 116 loop : -1.30 (0.20), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 539 TYR 0.033 0.001 TYR A 98 PHE 0.009 0.001 PHE B 540 TRP 0.007 0.001 TRP A 677 HIS 0.003 0.001 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00272 (20512) covalent geometry : angle 0.52765 (27816) hydrogen bonds : bond 0.02975 ( 1044) hydrogen bonds : angle 3.61611 ( 3096) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 299 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 LYS cc_start: 0.6360 (mmtm) cc_final: 0.5809 (mtmt) REVERT: A 111 TYR cc_start: 0.8061 (m-80) cc_final: 0.7770 (m-80) REVERT: A 148 ASN cc_start: 0.6557 (t0) cc_final: 0.6301 (t0) REVERT: A 163 GLN cc_start: 0.7583 (tt0) cc_final: 0.6993 (tp40) REVERT: A 173 GLU cc_start: 0.8303 (tp30) cc_final: 0.8066 (tp30) REVERT: A 205 THR cc_start: 0.9071 (t) cc_final: 0.8701 (m) REVERT: A 277 MET cc_start: 0.8893 (tpp) cc_final: 0.8341 (mmt) REVERT: A 345 LEU cc_start: 0.8781 (pp) cc_final: 0.8561 (mt) REVERT: A 375 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8587 (pp) REVERT: A 383 GLN cc_start: 0.8436 (tp-100) cc_final: 0.7843 (tm-30) REVERT: A 591 ARG cc_start: 0.8361 (ptm160) cc_final: 0.7608 (mmm160) REVERT: A 634 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.7845 (m-80) REVERT: A 640 MET cc_start: 0.8388 (tmm) cc_final: 0.7892 (ttp) REVERT: B 104 LYS cc_start: 0.6212 (mmtm) cc_final: 0.5714 (mtmt) REVERT: B 111 TYR cc_start: 0.7979 (m-80) cc_final: 0.7742 (m-80) REVERT: B 163 GLN cc_start: 0.7631 (tt0) cc_final: 0.7070 (tp40) REVERT: B 173 GLU cc_start: 0.8324 (tp30) cc_final: 0.7967 (tp30) REVERT: B 205 THR cc_start: 0.9059 (t) cc_final: 0.8679 (m) REVERT: B 277 MET cc_start: 0.8873 (tpp) cc_final: 0.8339 (mmt) REVERT: B 375 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8634 (pp) REVERT: B 383 GLN cc_start: 0.8417 (tp-100) cc_final: 0.7846 (tm-30) REVERT: B 591 ARG cc_start: 0.8392 (ptm160) cc_final: 0.7660 (mmp80) REVERT: B 634 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.7936 (m-80) REVERT: C 104 LYS cc_start: 0.6192 (mmtm) cc_final: 0.5703 (mtmt) REVERT: C 111 TYR cc_start: 0.8038 (m-80) cc_final: 0.7734 (m-80) REVERT: C 163 GLN cc_start: 0.7609 (tt0) cc_final: 0.7010 (tp40) REVERT: C 173 GLU cc_start: 0.8343 (tp30) cc_final: 0.7986 (tp30) REVERT: C 205 THR cc_start: 0.9082 (t) cc_final: 0.8717 (m) REVERT: C 277 MET cc_start: 0.8888 (tpp) cc_final: 0.8348 (mmt) REVERT: C 375 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8589 (pp) REVERT: C 383 GLN cc_start: 0.8420 (tp-100) cc_final: 0.7829 (tm-30) REVERT: C 405 PHE cc_start: 0.7672 (t80) cc_final: 0.7455 (m-10) REVERT: C 539 ARG cc_start: 0.7970 (mtp180) cc_final: 0.7630 (mtt-85) REVERT: C 591 ARG cc_start: 0.8365 (ptm160) cc_final: 0.7655 (mmp80) REVERT: C 634 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.7847 (m-80) REVERT: C 640 MET cc_start: 0.8447 (tmm) cc_final: 0.7859 (ttp) REVERT: C 645 MET cc_start: 0.7882 (tpp) cc_final: 0.7617 (tpp) REVERT: D 104 LYS cc_start: 0.6125 (mmtm) cc_final: 0.5655 (mtmt) REVERT: D 111 TYR cc_start: 0.8043 (m-80) cc_final: 0.7786 (m-80) REVERT: D 163 GLN cc_start: 0.7615 (tt0) cc_final: 0.7046 (tp40) REVERT: D 173 GLU cc_start: 0.8444 (tp30) cc_final: 0.7985 (tp30) REVERT: D 205 THR cc_start: 0.9069 (t) cc_final: 0.8698 (m) REVERT: D 277 MET cc_start: 0.8870 (tpp) cc_final: 0.8344 (mmt) REVERT: D 375 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8602 (pp) REVERT: D 383 GLN cc_start: 0.8431 (tp-100) cc_final: 0.7852 (tm-30) REVERT: D 539 ARG cc_start: 0.7915 (mtp180) cc_final: 0.7624 (mtt-85) REVERT: D 591 ARG cc_start: 0.8423 (ptm160) cc_final: 0.7647 (mmp80) REVERT: D 634 TYR cc_start: 0.8538 (OUTLIER) cc_final: 0.7922 (m-80) outliers start: 46 outliers final: 37 residues processed: 337 average time/residue: 0.1489 time to fit residues: 77.3764 Evaluate side-chains 342 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 297 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 375 LEU Chi-restraints excluded: chain A residue 502 VAL Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 621 VAL Chi-restraints excluded: chain A residue 634 TYR Chi-restraints excluded: chain A residue 656 SER Chi-restraints excluded: chain A residue 707 VAL Chi-restraints excluded: chain B residue 84 VAL Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain B residue 326 LEU Chi-restraints excluded: chain B residue 375 LEU Chi-restraints excluded: chain B residue 502 VAL Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 522 THR Chi-restraints excluded: chain B residue 533 ILE Chi-restraints excluded: chain B residue 621 VAL Chi-restraints excluded: chain B residue 634 TYR Chi-restraints excluded: chain B residue 707 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 184 VAL Chi-restraints excluded: chain C residue 326 LEU Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 502 VAL Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 522 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 621 VAL Chi-restraints excluded: chain C residue 634 TYR Chi-restraints excluded: chain C residue 707 VAL Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 326 LEU Chi-restraints excluded: chain D residue 375 LEU Chi-restraints excluded: chain D residue 502 VAL Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 522 THR Chi-restraints excluded: chain D residue 533 ILE Chi-restraints excluded: chain D residue 621 VAL Chi-restraints excluded: chain D residue 634 TYR Chi-restraints excluded: chain D residue 707 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 36 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 232 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 173 optimal weight: 0.7980 chunk 101 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 112 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3658 r_free = 0.3658 target = 0.142599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.115554 restraints weight = 26544.578| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.08 r_work: 0.3181 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 20512 Z= 0.113 Angle : 0.523 10.468 27816 Z= 0.259 Chirality : 0.038 0.173 3116 Planarity : 0.004 0.055 3428 Dihedral : 6.702 52.491 2772 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.21 % Allowed : 17.02 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.17), residues: 2412 helix: 2.08 (0.13), residues: 1432 sheet: -1.56 (0.46), residues: 116 loop : -1.26 (0.20), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 617 TYR 0.033 0.001 TYR A 98 PHE 0.009 0.001 PHE B 540 TRP 0.007 0.001 TRP A 677 HIS 0.003 0.001 HIS D 313 Details of bonding type rmsd covalent geometry : bond 0.00266 (20512) covalent geometry : angle 0.52289 (27816) hydrogen bonds : bond 0.02951 ( 1044) hydrogen bonds : angle 3.59708 ( 3096) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5309.08 seconds wall clock time: 91 minutes 37.67 seconds (5497.67 seconds total)