Starting phenix.real_space_refine on Thu Mar 5 06:37:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zn4_14800/03_2026/7zn4_14800.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zn4_14800/03_2026/7zn4_14800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zn4_14800/03_2026/7zn4_14800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zn4_14800/03_2026/7zn4_14800.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zn4_14800/03_2026/7zn4_14800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zn4_14800/03_2026/7zn4_14800.map" } resolution = 4.32 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= 0.001 sd= 0.004 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 50 5.16 5 C 12717 2.51 5 N 3348 2.21 5 O 3874 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 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: 19989 Number of models: 1 Model: "" Number of chains: 6 Chain: "d" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1688 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Chain: "b" Number of atoms: 1761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1761 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 13, 'TRANS': 210} Chain: "f" Number of atoms: 5143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5143 Classifications: {'peptide': 669} Link IDs: {'PTRANS': 34, 'TRANS': 634} Chain breaks: 2 Chain: "e" Number of atoms: 5163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 671, 5163 Classifications: {'peptide': 671} Link IDs: {'PTRANS': 34, 'TRANS': 636} Chain breaks: 2 Chain: "g" Number of atoms: 4546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 589, 4546 Classifications: {'peptide': 589} Link IDs: {'PTRANS': 26, 'TRANS': 562} Chain breaks: 2 Chain: "c" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1688 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Time building chain proxies: 4.59, per 1000 atoms: 0.23 Number of scatterers: 19989 At special positions: 0 Unit cell: (214.809, 148.61, 124.292, 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 50 16.00 O 3874 8.00 N 3348 7.00 C 12717 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: 1.60 Conformation dependent library (CDL) restraints added in 805.4 milliseconds 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4738 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 44 sheets defined 7.0% alpha, 25.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'd' and resid 907 through 914 removed outlier: 3.590A pdb=" N ASN d 911 " --> pdb=" O LEU d 907 " (cutoff:3.500A) Processing helix chain 'b' and resid 907 through 913 Processing helix chain 'b' and resid 914 through 921 removed outlier: 3.677A pdb=" N LEU b 918 " --> pdb=" O ASP b 914 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 90 Processing helix chain 'f' and resid 258 through 264 Processing helix chain 'f' and resid 302 through 305 Processing helix chain 'f' and resid 325 through 330 removed outlier: 3.640A pdb=" N ASN f 329 " --> pdb=" O ASN f 325 " (cutoff:3.500A) Processing helix chain 'f' and resid 579 through 592 Processing helix chain 'f' and resid 661 through 667 Processing helix chain 'f' and resid 669 through 673 Processing helix chain 'e' and resid 83 through 90 Processing helix chain 'e' and resid 258 through 264 Processing helix chain 'e' and resid 325 through 330 Processing helix chain 'e' and resid 579 through 591 Processing helix chain 'e' and resid 662 through 668 Processing helix chain 'g' and resid 83 through 90 Processing helix chain 'g' and resid 258 through 265 Processing helix chain 'g' and resid 302 through 305 Processing helix chain 'g' and resid 325 through 330 removed outlier: 4.353A pdb=" N ASN g 329 " --> pdb=" O ASN g 325 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU g 330 " --> pdb=" O SER g 326 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 325 through 330' Processing helix chain 'g' and resid 579 through 591 removed outlier: 3.723A pdb=" N ALA g 583 " --> pdb=" O ASN g 579 " (cutoff:3.500A) Processing helix chain 'g' and resid 661 through 667 Processing helix chain 'g' and resid 669 through 673 removed outlier: 3.580A pdb=" N GLY g 672 " --> pdb=" O ASN g 669 " (cutoff:3.500A) Processing helix chain 'c' and resid 907 through 914 Processing helix chain 'c' and resid 915 through 921 Processing sheet with id=AA1, first strand: chain 'd' and resid 742 through 745 removed outlier: 3.655A pdb=" N LYS d 743 " --> pdb=" O SER d 762 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N SER d 762 " --> pdb=" O LYS d 743 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR d 745 " --> pdb=" O GLU d 760 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU d 760 " --> pdb=" O THR d 745 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TRP d 763 " --> pdb=" O MET d 798 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'd' and resid 785 through 788 removed outlier: 3.685A pdb=" N ALA d 777 " --> pdb=" O GLU d 813 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLU d 813 " --> pdb=" O ALA d 777 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA d 810 " --> pdb=" O VAL d 831 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL d 831 " --> pdb=" O ALA d 810 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL d 827 " --> pdb=" O LEU d 814 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'd' and resid 845 through 847 Processing sheet with id=AA4, first strand: chain 'd' and resid 892 through 898 removed outlier: 3.533A pdb=" N ARG d 894 " --> pdb=" O ILE d 885 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG d 932 " --> pdb=" O GLU d 884 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'b' and resid 731 through 734 removed outlier: 3.672A pdb=" N GLU c 899 " --> pdb=" O ASP b 731 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE c 885 " --> pdb=" O LEU c 893 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER c 895 " --> pdb=" O LEU c 883 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N LEU c 883 " --> pdb=" O SER c 895 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N ARG c 897 " --> pdb=" O TYR c 881 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR c 881 " --> pdb=" O ARG c 897 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLU c 899 " --> pdb=" O ILE c 879 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ILE c 879 " --> pdb=" O GLU c 899 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'b' and resid 743 through 745 Processing sheet with id=AA7, first strand: chain 'b' and resid 785 through 788 removed outlier: 4.279A pdb=" N TYR b 773 " --> pdb=" O VAL b 817 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL b 817 " --> pdb=" O TYR b 773 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU b 813 " --> pdb=" O ALA b 777 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'b' and resid 846 through 847 Processing sheet with id=AA9, first strand: chain 'b' and resid 893 through 899 removed outlier: 3.509A pdb=" N ILE b 885 " --> pdb=" O LEU b 893 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N SER b 895 " --> pdb=" O LEU b 883 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU b 883 " --> pdb=" O SER b 895 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ARG b 897 " --> pdb=" O TYR b 881 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR b 881 " --> pdb=" O ARG b 897 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLU b 899 " --> pdb=" O ILE b 879 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N ILE b 879 " --> pdb=" O GLU b 899 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 16 through 18 Processing sheet with id=AB2, first strand: chain 'f' and resid 46 through 52 removed outlier: 3.872A pdb=" N GLY f 36 " --> pdb=" O TYR f 78 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'f' and resid 71 through 72 removed outlier: 3.990A pdb=" N PHE f 101 " --> pdb=" O TYR f 71 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'f' and resid 108 through 116 removed outlier: 6.506A pdb=" N ASP f 131 " --> pdb=" O THR f 110 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA f 112 " --> pdb=" O TYR f 129 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N TYR f 129 " --> pdb=" O ALA f 112 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N CYS f 114 " --> pdb=" O ILE f 127 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE f 127 " --> pdb=" O CYS f 114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'f' and resid 153 through 157 removed outlier: 5.638A pdb=" N LYS f 155 " --> pdb=" O LEU f 143 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N LEU f 143 " --> pdb=" O LYS f 155 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TYR f 138 " --> pdb=" O GLN f 182 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN f 182 " --> pdb=" O TYR f 138 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR f 140 " --> pdb=" O SER f 180 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'f' and resid 173 through 175 Processing sheet with id=AB7, first strand: chain 'f' and resid 217 through 222 removed outlier: 4.044A pdb=" N ASN f 217 " --> pdb=" O ASP f 239 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN f 237 " --> pdb=" O VAL f 219 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'f' and resid 250 through 257 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 271 through 274 current: chain 'f' and resid 307 through 309 Processing sheet with id=AB9, first strand: chain 'f' and resid 331 through 335 removed outlier: 6.411A pdb=" N ILE f 340 " --> pdb=" O LEU f 355 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N LEU f 355 " --> pdb=" O ILE f 340 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLY f 342 " --> pdb=" O THR f 353 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'f' and resid 376 through 379 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 384 through 387 current: chain 'f' and resid 428 through 433 removed outlier: 3.535A pdb=" N GLY f 431 " --> pdb=" O LYS f 440 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 457 through 459 current: chain 'f' and resid 627 through 629 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 627 through 629 current: chain 'f' and resid 676 through 679 WARNING: can't find start of bonding for strands! previous: chain 'f' and resid 684 through 687 current: chain 'e' and resid 339 through 346 removed outlier: 6.998A pdb=" N ILE e 340 " --> pdb=" O LEU e 355 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU e 355 " --> pdb=" O ILE e 340 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N GLY e 342 " --> pdb=" O THR e 353 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE e 376 " --> pdb=" O ILE e 365 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 384 through 393 current: chain 'e' and resid 427 through 433 removed outlier: 3.739A pdb=" N GLY e 427 " --> pdb=" O GLY e 444 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS e 438 " --> pdb=" O ASP e 433 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 457 through 459 current: chain 'e' and resid 627 through 629 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 627 through 629 current: chain 'e' and resid 677 through 678 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 677 through 678 current: chain 'g' and resid 339 through 345 removed outlier: 3.587A pdb=" N PHE g 354 " --> pdb=" O GLY g 342 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ILE g 344 " --> pdb=" O GLN g 352 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N GLN g 352 " --> pdb=" O ILE g 344 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE g 363 " --> pdb=" O PHE g 378 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE g 376 " --> pdb=" O ILE g 365 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 384 through 387 current: chain 'g' and resid 427 through 431 removed outlier: 3.546A pdb=" N GLY g 427 " --> pdb=" O GLY g 444 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 456 through 459 current: chain 'g' and resid 627 through 629 Processing sheet with id=AC2, first strand: chain 'f' and resid 484 through 488 removed outlier: 3.876A pdb=" N TYR f 487 " --> pdb=" O ILE f 521 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE f 521 " --> pdb=" O TYR f 487 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'f' and resid 528 through 529 removed outlier: 3.556A pdb=" N GLN f 534 " --> pdb=" O ASP f 529 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'f' and resid 567 through 572 Processing sheet with id=AC5, first strand: chain 'e' and resid 12 through 17 Processing sheet with id=AC6, first strand: chain 'e' and resid 47 through 53 removed outlier: 4.025A pdb=" N ARG e 37 " --> pdb=" O PHE e 52 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'e' and resid 71 through 73 Processing sheet with id=AC8, first strand: chain 'e' and resid 109 through 113 removed outlier: 6.718A pdb=" N ASP e 131 " --> pdb=" O THR e 110 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ALA e 112 " --> pdb=" O TYR e 129 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N TYR e 129 " --> pdb=" O ALA e 112 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'e' and resid 138 through 145 removed outlier: 7.056A pdb=" N CYS e 139 " --> pdb=" O VAL e 158 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N VAL e 158 " --> pdb=" O CYS e 139 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ILE e 141 " --> pdb=" O TYR e 156 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 154 through 159 current: chain 'e' and resid 191 through 192 Processing sheet with id=AD1, first strand: chain 'e' and resid 216 through 222 removed outlier: 4.236A pdb=" N ILE e 218 " --> pdb=" O GLN e 237 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLN e 237 " --> pdb=" O ILE e 218 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N PHE e 220 " --> pdb=" O ARG e 235 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ARG e 235 " --> pdb=" O PHE e 220 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'e' and resid 248 through 257 WARNING: can't find start of bonding for strands! previous: chain 'e' and resid 270 through 274 current: chain 'e' and resid 308 through 309 Processing sheet with id=AD3, first strand: chain 'e' and resid 481 through 482 removed outlier: 3.513A pdb=" N GLN e 534 " --> pdb=" O ASP e 529 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'e' and resid 485 through 486 removed outlier: 4.006A pdb=" N PHE e 485 " --> pdb=" O CYS e 523 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N CYS e 523 " --> pdb=" O PHE e 485 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'e' and resid 567 through 572 removed outlier: 3.599A pdb=" N ASP e 599 " --> pdb=" O TRP e 617 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N THR e 611 " --> pdb=" O LYS e 605 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'g' and resid 12 through 14 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 12 through 14 current: chain 'g' and resid 21 through 26 Processing sheet with id=AD7, first strand: chain 'g' and resid 46 through 53 removed outlier: 3.634A pdb=" N GLY g 36 " --> pdb=" O TYR g 78 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'g' and resid 108 through 116 removed outlier: 5.363A pdb=" N ILE g 109 " --> pdb=" O THR g 133 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N THR g 133 " --> pdb=" O ILE g 109 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'g' and resid 138 through 139 removed outlier: 3.642A pdb=" N TYR g 138 " --> pdb=" O GLN g 182 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N THR g 190 " --> pdb=" O LEU g 185 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'g' and resid 141 through 145 removed outlier: 7.005A pdb=" N ILE g 141 " --> pdb=" O TYR g 156 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 154 through 157 current: chain 'g' and resid 197 through 198 Processing sheet with id=AE2, first strand: chain 'g' and resid 217 through 223 removed outlier: 3.687A pdb=" N ASN g 217 " --> pdb=" O ASP g 239 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA g 223 " --> pdb=" O ASP g 233 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'g' and resid 252 through 257 WARNING: can't find start of bonding for strands! previous: chain 'g' and resid 270 through 273 current: chain 'g' and resid 307 through 309 Processing sheet with id=AE4, first strand: chain 'g' and resid 567 through 572 removed outlier: 4.170A pdb=" N LYS g 605 " --> pdb=" O THR g 611 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR g 611 " --> pdb=" O LYS g 605 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'g' and resid 675 through 678 removed outlier: 3.613A pdb=" N ILE g 678 " --> pdb=" O TYR g 684 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'c' and resid 740 through 745 removed outlier: 3.846A pdb=" N PHE c 742 " --> pdb=" O SER c 762 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N SER c 762 " --> pdb=" O PHE c 742 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N TYR c 744 " --> pdb=" O GLU c 760 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLU c 760 " --> pdb=" O TYR c 744 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 785 through 788 Processing sheet with id=AE8, first strand: chain 'c' and resid 845 through 847 451 hydrogen bonds defined for protein. 1173 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: 3.73 Time building geometry restraints manager: 2.12 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: 6517 1.34 - 1.46: 4266 1.46 - 1.57: 9571 1.57 - 1.69: 0 1.69 - 1.81: 92 Bond restraints: 20446 Sorted by residual: bond pdb=" N MET f 1 " pdb=" CA MET f 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.82e+00 bond pdb=" N MET e 1 " pdb=" CA MET e 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.80e+00 bond pdb=" N MET g 1 " pdb=" CA MET g 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.75e+00 bond pdb=" C PRO e 511 " pdb=" N PRO e 512 " ideal model delta sigma weight residual 1.326 1.341 -0.015 1.44e-02 4.82e+03 1.10e+00 bond pdb=" C THR b 747 " pdb=" N PRO b 748 " ideal model delta sigma weight residual 1.331 1.340 -0.008 7.90e-03 1.60e+04 1.06e+00 ... (remaining 20441 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 27081 1.17 - 2.35: 585 2.35 - 3.52: 142 3.52 - 4.69: 60 4.69 - 5.87: 3 Bond angle restraints: 27871 Sorted by residual: angle pdb=" N TYR e 487 " pdb=" CA TYR e 487 " pdb=" C TYR e 487 " ideal model delta sigma weight residual 111.71 117.00 -5.29 1.34e+00 5.57e-01 1.56e+01 angle pdb=" N TYR e 487 " pdb=" CA TYR e 487 " pdb=" CB TYR e 487 " ideal model delta sigma weight residual 111.66 105.79 5.87 1.56e+00 4.11e-01 1.41e+01 angle pdb=" N LYS g 677 " pdb=" CA LYS g 677 " pdb=" C LYS g 677 " ideal model delta sigma weight residual 110.65 107.07 3.58 1.26e+00 6.30e-01 8.07e+00 angle pdb=" CA TYR e 487 " pdb=" C TYR e 487 " pdb=" N ILE e 488 " ideal model delta sigma weight residual 117.40 120.34 -2.94 1.41e+00 5.03e-01 4.35e+00 angle pdb=" C GLU d 899 " pdb=" N ASP d 900 " pdb=" CA ASP d 900 " ideal model delta sigma weight residual 121.54 125.47 -3.93 1.91e+00 2.74e-01 4.23e+00 ... (remaining 27866 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 11144 17.91 - 35.82: 795 35.82 - 53.72: 106 53.72 - 71.63: 15 71.63 - 89.54: 10 Dihedral angle restraints: 12070 sinusoidal: 4640 harmonic: 7430 Sorted by residual: dihedral pdb=" CA ILE e 486 " pdb=" C ILE e 486 " pdb=" N TYR e 487 " pdb=" CA TYR e 487 " ideal model delta harmonic sigma weight residual -180.00 -151.90 -28.10 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA LYS e 675 " pdb=" C LYS e 675 " pdb=" N MET e 676 " pdb=" CA MET e 676 " ideal model delta harmonic sigma weight residual 180.00 -155.31 -24.69 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA TYR e 502 " pdb=" C TYR e 502 " pdb=" N PRO e 503 " pdb=" CA PRO e 503 " ideal model delta harmonic sigma weight residual 180.00 158.12 21.88 0 5.00e+00 4.00e-02 1.91e+01 ... (remaining 12067 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1954 0.031 - 0.062: 704 0.062 - 0.093: 164 0.093 - 0.124: 271 0.124 - 0.155: 40 Chirality restraints: 3133 Sorted by residual: chirality pdb=" CA ILE e 489 " pdb=" N ILE e 489 " pdb=" C ILE e 489 " pdb=" CB ILE e 489 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.03e-01 chirality pdb=" CA ILE e 486 " pdb=" N ILE e 486 " pdb=" C ILE e 486 " pdb=" CB ILE e 486 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.32e-01 chirality pdb=" CA VAL f 484 " pdb=" N VAL f 484 " pdb=" C VAL f 484 " pdb=" CB VAL f 484 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.90e-01 ... (remaining 3130 not shown) Planarity restraints: 3604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP e 507 " -0.016 2.00e-02 2.50e+03 1.96e-02 9.65e+00 pdb=" CG TRP e 507 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP e 507 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP e 507 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP e 507 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP e 507 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP e 507 " -0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP e 507 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP e 507 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP e 507 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR f 502 " -0.036 5.00e-02 4.00e+02 5.39e-02 4.64e+00 pdb=" N PRO f 503 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO f 503 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO f 503 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS c 912 " 0.010 2.00e-02 2.50e+03 2.00e-02 4.01e+00 pdb=" C LYS c 912 " -0.035 2.00e-02 2.50e+03 pdb=" O LYS c 912 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA c 913 " 0.012 2.00e-02 2.50e+03 ... (remaining 3601 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 397 2.63 - 3.20: 19441 3.20 - 3.77: 31796 3.77 - 4.33: 44449 4.33 - 4.90: 72045 Nonbonded interactions: 168128 Sorted by model distance: nonbonded pdb=" O VAL c 855 " pdb=" OG1 THR c 856 " model vdw 2.063 3.040 nonbonded pdb=" O ILE f 474 " pdb=" OG SER g 193 " model vdw 2.068 3.040 nonbonded pdb=" NH2 ARG d 932 " pdb=" O TRP d 946 " model vdw 2.095 3.120 nonbonded pdb=" OG1 THR c 745 " pdb=" OE2 GLU c 760 " model vdw 2.103 3.040 nonbonded pdb=" NH1 ARG e 242 " pdb=" O GLY e 245 " model vdw 2.109 3.120 ... (remaining 168123 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'b' and resid 736 through 949) selection = chain 'c' selection = chain 'd' } ncs_group { reference = (chain 'e' and (resid 1 through 223 or resid 232 through 469 or resid 562 throug \ h 688)) selection = (chain 'f' and (resid 1 through 469 or resid 562 through 688)) selection = (chain 'g' and (resid 1 through 223 or resid 232 through 688)) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.320 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: 0.020 Extract box with map and model: 0.200 Check model and map are aligned: 0.080 Set scattering table: 0.030 Process input model: 19.140 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.050 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:1.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 : 0.003 0.032 20446 Z= 0.126 Angle : 0.491 5.865 27871 Z= 0.264 Chirality : 0.046 0.155 3133 Planarity : 0.003 0.054 3604 Dihedral : 12.383 89.540 7332 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.60 (0.16), residues: 2557 helix: 0.20 (0.43), residues: 175 sheet: 0.33 (0.19), residues: 791 loop : -0.86 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 815 TYR 0.017 0.001 TYR f 487 PHE 0.010 0.001 PHE f 52 TRP 0.052 0.001 TRP e 507 HIS 0.002 0.001 HIS d 778 Details of bonding type rmsd covalent geometry : bond 0.00252 (20446) covalent geometry : angle 0.49131 (27871) hydrogen bonds : bond 0.25651 ( 451) hydrogen bonds : angle 10.07304 ( 1173) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 168 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 815 ARG cc_start: 0.7305 (tpm170) cc_final: 0.6823 (tpp-160) REVERT: d 833 LEU cc_start: 0.7936 (tt) cc_final: 0.7648 (mp) REVERT: b 892 MET cc_start: 0.6414 (tpt) cc_final: 0.6070 (tpt) REVERT: f 10 MET cc_start: 0.8162 (ttm) cc_final: 0.7942 (ttt) REVERT: f 403 MET cc_start: 0.8640 (mtm) cc_final: 0.8407 (ptp) REVERT: f 432 MET cc_start: 0.8409 (mmm) cc_final: 0.8013 (tpp) REVERT: f 676 MET cc_start: 0.8463 (ttp) cc_final: 0.7931 (ttp) REVERT: e 430 MET cc_start: 0.7822 (ttm) cc_final: 0.7320 (tmm) REVERT: g 633 MET cc_start: 0.7802 (ttt) cc_final: 0.7309 (ttm) REVERT: g 676 MET cc_start: 0.5887 (mpp) cc_final: 0.5245 (ttm) REVERT: c 798 MET cc_start: 0.5197 (pmm) cc_final: 0.4902 (pmm) REVERT: c 915 PHE cc_start: 0.7717 (m-10) cc_final: 0.6821 (m-80) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.1406 time to fit residues: 37.4609 Evaluate side-chains 92 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 182 GLN ** f 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 417 GLN f 479 GLN e 237 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.047290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.038196 restraints weight = 122125.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.038926 restraints weight = 69815.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.039201 restraints weight = 42361.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.039515 restraints weight = 36204.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.039473 restraints weight = 30840.489| |-----------------------------------------------------------------------------| r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2846 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2846 r_free = 0.2846 target_work(ls_wunit_k1) = 0.039 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2846 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20446 Z= 0.149 Angle : 0.553 11.335 27871 Z= 0.297 Chirality : 0.049 0.180 3133 Planarity : 0.004 0.043 3604 Dihedral : 4.469 32.049 2786 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 0.09 % Allowed : 4.27 % Favored : 95.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.46 (0.16), residues: 2557 helix: 0.67 (0.45), residues: 166 sheet: 0.29 (0.19), residues: 783 loop : -0.71 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG d 815 TYR 0.031 0.001 TYR f 138 PHE 0.015 0.002 PHE e 327 TRP 0.015 0.001 TRP d 946 HIS 0.005 0.001 HIS d 781 Details of bonding type rmsd covalent geometry : bond 0.00334 (20446) covalent geometry : angle 0.55289 (27871) hydrogen bonds : bond 0.04278 ( 451) hydrogen bonds : angle 7.57883 ( 1173) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 113 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 833 LEU cc_start: 0.8299 (tt) cc_final: 0.7968 (mp) REVERT: d 890 ASP cc_start: 0.7707 (t0) cc_final: 0.6965 (p0) REVERT: d 892 MET cc_start: 0.8209 (tmm) cc_final: 0.7960 (tmm) REVERT: b 892 MET cc_start: 0.6214 (tpt) cc_final: 0.5985 (tpt) REVERT: f 633 MET cc_start: 0.8657 (tpp) cc_final: 0.8412 (tpp) REVERT: f 676 MET cc_start: 0.8296 (ttp) cc_final: 0.7743 (ttp) REVERT: e 430 MET cc_start: 0.7916 (ttm) cc_final: 0.7618 (tmm) REVERT: g 10 MET cc_start: 0.7581 (ptp) cc_final: 0.7006 (pmm) REVERT: g 430 MET cc_start: 0.8080 (ttp) cc_final: 0.7849 (ptm) REVERT: g 633 MET cc_start: 0.7858 (ttt) cc_final: 0.7595 (ttt) REVERT: g 676 MET cc_start: 0.5626 (mpp) cc_final: 0.5086 (ttm) REVERT: c 798 MET cc_start: 0.6612 (pmm) cc_final: 0.6343 (pmm) REVERT: c 915 PHE cc_start: 0.7440 (m-10) cc_final: 0.6773 (m-80) outliers start: 2 outliers final: 1 residues processed: 115 average time/residue: 0.1287 time to fit residues: 24.5303 Evaluate side-chains 87 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 184 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 131 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 229 optimal weight: 1.9990 chunk 4 optimal weight: 0.0020 chunk 34 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 158 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 278 GLN ** c 789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.046506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.037243 restraints weight = 123653.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.038008 restraints weight = 68271.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.038336 restraints weight = 40869.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.038517 restraints weight = 35529.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.038543 restraints weight = 30771.459| |-----------------------------------------------------------------------------| r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2810 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2810 r_free = 0.2810 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2810 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 20446 Z= 0.164 Angle : 0.539 10.011 27871 Z= 0.288 Chirality : 0.048 0.255 3133 Planarity : 0.004 0.047 3604 Dihedral : 4.535 31.419 2786 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.58 (0.16), residues: 2557 helix: 0.65 (0.46), residues: 159 sheet: 0.16 (0.19), residues: 792 loop : -0.78 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 894 TYR 0.034 0.002 TYR f 138 PHE 0.013 0.002 PHE e 485 TRP 0.028 0.001 TRP e 507 HIS 0.003 0.001 HIS d 778 Details of bonding type rmsd covalent geometry : bond 0.00369 (20446) covalent geometry : angle 0.53928 (27871) hydrogen bonds : bond 0.03830 ( 451) hydrogen bonds : angle 6.95215 ( 1173) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 798 MET cc_start: 0.3028 (ptt) cc_final: 0.2613 (ptt) REVERT: d 815 ARG cc_start: 0.7851 (tpm170) cc_final: 0.7273 (tpp-160) REVERT: d 833 LEU cc_start: 0.8397 (tt) cc_final: 0.8106 (mp) REVERT: f 676 MET cc_start: 0.8348 (ttp) cc_final: 0.7977 (ttp) REVERT: e 430 MET cc_start: 0.7921 (ttm) cc_final: 0.7388 (tmm) REVERT: e 432 MET cc_start: 0.8245 (mmp) cc_final: 0.7899 (mmm) REVERT: g 676 MET cc_start: 0.5812 (mpp) cc_final: 0.5530 (ttt) REVERT: c 788 GLN cc_start: 0.6677 (pt0) cc_final: 0.6416 (tp-100) REVERT: c 915 PHE cc_start: 0.7604 (m-10) cc_final: 0.6722 (m-10) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.1295 time to fit residues: 22.8390 Evaluate side-chains 77 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 149 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 179 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 191 optimal weight: 0.2980 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 234 optimal weight: 20.0000 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN g 417 GLN c 789 GLN ** c 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.046445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.037085 restraints weight = 122793.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.037925 restraints weight = 70038.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.038269 restraints weight = 40211.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.038373 restraints weight = 36120.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.038455 restraints weight = 31449.348| |-----------------------------------------------------------------------------| r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20446 Z= 0.144 Angle : 0.531 10.404 27871 Z= 0.280 Chirality : 0.048 0.244 3133 Planarity : 0.004 0.056 3604 Dihedral : 4.488 29.574 2786 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.58 (0.16), residues: 2557 helix: 0.57 (0.46), residues: 160 sheet: 0.17 (0.18), residues: 804 loop : -0.78 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG f 49 TYR 0.035 0.001 TYR f 138 PHE 0.015 0.001 PHE f 586 TRP 0.010 0.001 TRP d 946 HIS 0.004 0.001 HIS d 778 Details of bonding type rmsd covalent geometry : bond 0.00325 (20446) covalent geometry : angle 0.53066 (27871) hydrogen bonds : bond 0.03212 ( 451) hydrogen bonds : angle 6.64305 ( 1173) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 798 MET cc_start: 0.3039 (ptt) cc_final: 0.2605 (ptt) REVERT: d 815 ARG cc_start: 0.7851 (tpm170) cc_final: 0.7252 (tpp-160) REVERT: f 633 MET cc_start: 0.8730 (tpp) cc_final: 0.8420 (tpp) REVERT: f 676 MET cc_start: 0.8299 (ttp) cc_final: 0.8010 (ttp) REVERT: e 430 MET cc_start: 0.7926 (ttm) cc_final: 0.7371 (tmm) REVERT: e 432 MET cc_start: 0.8146 (mmp) cc_final: 0.7877 (mmm) REVERT: e 627 MET cc_start: 0.9122 (tmm) cc_final: 0.8654 (ttp) REVERT: e 633 MET cc_start: 0.8388 (ttm) cc_final: 0.8155 (ttm) REVERT: g 676 MET cc_start: 0.5884 (mpp) cc_final: 0.5575 (ttt) REVERT: c 788 GLN cc_start: 0.6811 (pt0) cc_final: 0.6511 (mm-40) REVERT: c 789 GLN cc_start: 0.4791 (mt0) cc_final: 0.4589 (mt0) REVERT: c 915 PHE cc_start: 0.7547 (m-10) cc_final: 0.6649 (m-10) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.1239 time to fit residues: 20.8856 Evaluate side-chains 77 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 197 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 159 optimal weight: 4.9990 chunk 217 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 145 optimal weight: 10.0000 chunk 214 optimal weight: 0.0980 chunk 71 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 70 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 overall best weight: 4.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 417 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN e 616 GLN g 148 ASN g 278 GLN g 579 ASN ** c 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.044465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.034919 restraints weight = 125217.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.035706 restraints weight = 71114.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2737 r_free = 0.2737 target = 0.036220 restraints weight = 47123.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.036512 restraints weight = 35376.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.036762 restraints weight = 29563.197| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2747 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2747 r_free = 0.2747 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2747 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 20446 Z= 0.296 Angle : 0.659 10.797 27871 Z= 0.351 Chirality : 0.050 0.384 3133 Planarity : 0.005 0.059 3604 Dihedral : 5.136 31.628 2786 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 (0.16), residues: 2557 helix: 0.14 (0.42), residues: 159 sheet: -0.03 (0.18), residues: 821 loop : -1.09 (0.15), residues: 1577 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG g 206 TYR 0.028 0.002 TYR f 138 PHE 0.030 0.003 PHE e 485 TRP 0.020 0.002 TRP e 541 HIS 0.007 0.002 HIS e 26 Details of bonding type rmsd covalent geometry : bond 0.00665 (20446) covalent geometry : angle 0.65900 (27871) hydrogen bonds : bond 0.03702 ( 451) hydrogen bonds : angle 6.80626 ( 1173) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 778 HIS cc_start: 0.5639 (t-170) cc_final: 0.5324 (t-170) REVERT: d 798 MET cc_start: 0.3458 (ptt) cc_final: 0.3125 (ptt) REVERT: d 890 ASP cc_start: 0.7460 (t0) cc_final: 0.6855 (p0) REVERT: d 892 MET cc_start: 0.8393 (tmm) cc_final: 0.7966 (tmm) REVERT: b 788 GLN cc_start: 0.6492 (tm-30) cc_final: 0.6013 (tm-30) REVERT: f 633 MET cc_start: 0.8803 (tpp) cc_final: 0.8521 (tpp) REVERT: f 676 MET cc_start: 0.8314 (ttp) cc_final: 0.7943 (ttp) REVERT: e 430 MET cc_start: 0.7949 (ttm) cc_final: 0.7397 (tmm) REVERT: e 432 MET cc_start: 0.8123 (mmp) cc_final: 0.7795 (mmm) REVERT: e 627 MET cc_start: 0.9144 (tmm) cc_final: 0.8754 (ttp) REVERT: e 633 MET cc_start: 0.8519 (ttm) cc_final: 0.8146 (ttm) REVERT: g 676 MET cc_start: 0.6243 (mpp) cc_final: 0.6041 (ttt) REVERT: c 915 PHE cc_start: 0.7808 (m-10) cc_final: 0.6888 (m-10) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1210 time to fit residues: 19.2233 Evaluate side-chains 69 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 128 optimal weight: 7.9990 chunk 148 optimal weight: 0.0070 chunk 109 optimal weight: 0.0970 chunk 104 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 248 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 270 GLN ** f 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN g 616 GLN c 919 ASN ** c 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.046278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.037021 restraints weight = 121264.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.037741 restraints weight = 66888.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.038011 restraints weight = 40854.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.038243 restraints weight = 35149.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.038237 restraints weight = 31068.032| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2801 r_free = 0.2801 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.2897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 20446 Z= 0.108 Angle : 0.536 9.796 27871 Z= 0.284 Chirality : 0.048 0.211 3133 Planarity : 0.004 0.070 3604 Dihedral : 4.680 33.174 2786 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: 2557 helix: 0.52 (0.45), residues: 154 sheet: 0.01 (0.18), residues: 848 loop : -0.86 (0.15), residues: 1555 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 206 TYR 0.029 0.001 TYR f 138 PHE 0.022 0.001 PHE c 742 TRP 0.010 0.001 TRP d 946 HIS 0.005 0.001 HIS d 778 Details of bonding type rmsd covalent geometry : bond 0.00245 (20446) covalent geometry : angle 0.53602 (27871) hydrogen bonds : bond 0.03077 ( 451) hydrogen bonds : angle 6.45781 ( 1173) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 815 ARG cc_start: 0.7826 (tpm170) cc_final: 0.7259 (tpp-160) REVERT: d 890 ASP cc_start: 0.7981 (t0) cc_final: 0.7270 (p0) REVERT: b 788 GLN cc_start: 0.6645 (tm-30) cc_final: 0.6224 (tm-30) REVERT: f 507 TRP cc_start: 0.5547 (m-10) cc_final: 0.4552 (m-10) REVERT: f 627 MET cc_start: 0.8526 (tpp) cc_final: 0.8291 (tpp) REVERT: f 676 MET cc_start: 0.8317 (ttp) cc_final: 0.8044 (ttp) REVERT: e 430 MET cc_start: 0.7971 (ttm) cc_final: 0.7467 (tmm) REVERT: e 432 MET cc_start: 0.8112 (mmp) cc_final: 0.7709 (mmm) REVERT: e 627 MET cc_start: 0.9173 (tmm) cc_final: 0.8683 (ttp) REVERT: g 10 MET cc_start: 0.7850 (ptp) cc_final: 0.7300 (pmm) REVERT: g 629 LEU cc_start: 0.9161 (mp) cc_final: 0.8954 (mm) REVERT: g 676 MET cc_start: 0.6294 (mpp) cc_final: 0.5922 (mtp) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1346 time to fit residues: 22.3837 Evaluate side-chains 75 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 68 optimal weight: 5.9990 chunk 105 optimal weight: 0.0470 chunk 92 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 171 optimal weight: 2.9990 chunk 189 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 135 optimal weight: 10.0000 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 455 ASN e 479 GLN ** g 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 778 HIS c 789 GLN c 919 ASN ** c 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.044854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.035517 restraints weight = 124982.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2734 r_free = 0.2734 target = 0.036164 restraints weight = 69292.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.036535 restraints weight = 43016.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.036624 restraints weight = 38200.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.036673 restraints weight = 34044.935| |-----------------------------------------------------------------------------| r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 20446 Z= 0.237 Angle : 0.610 10.725 27871 Z= 0.322 Chirality : 0.050 0.291 3133 Planarity : 0.005 0.058 3604 Dihedral : 5.004 33.947 2786 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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 (0.16), residues: 2557 helix: 0.23 (0.42), residues: 159 sheet: -0.10 (0.19), residues: 799 loop : -1.05 (0.15), residues: 1599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG b 894 TYR 0.021 0.002 TYR f 138 PHE 0.019 0.002 PHE e 485 TRP 0.022 0.002 TRP d 946 HIS 0.008 0.001 HIS e 26 Details of bonding type rmsd covalent geometry : bond 0.00538 (20446) covalent geometry : angle 0.60994 (27871) hydrogen bonds : bond 0.03304 ( 451) hydrogen bonds : angle 6.59094 ( 1173) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 778 HIS cc_start: 0.5995 (t-170) cc_final: 0.5683 (t-170) REVERT: b 788 GLN cc_start: 0.6504 (tm-30) cc_final: 0.6015 (tm-30) REVERT: b 798 MET cc_start: 0.5754 (ptt) cc_final: 0.5550 (ptt) REVERT: f 676 MET cc_start: 0.8221 (ttp) cc_final: 0.7967 (ttp) REVERT: e 430 MET cc_start: 0.7887 (ttm) cc_final: 0.7381 (tmm) REVERT: g 456 ILE cc_start: 0.8667 (tt) cc_final: 0.8441 (mt) REVERT: g 676 MET cc_start: 0.6533 (mpp) cc_final: 0.6146 (mtp) REVERT: c 742 PHE cc_start: 0.7215 (t80) cc_final: 0.6842 (t80) REVERT: c 915 PHE cc_start: 0.7630 (m-10) cc_final: 0.6628 (m-10) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.1162 time to fit residues: 17.7991 Evaluate side-chains 68 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 8.9990 chunk 246 optimal weight: 2.9990 chunk 252 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 61 optimal weight: 0.9980 chunk 76 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 13 optimal weight: 7.9990 chunk 141 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 789 GLN ** d 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 911 ASN ** f 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN ** g 686 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 781 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.044091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.035189 restraints weight = 125992.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.035665 restraints weight = 72116.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.035939 restraints weight = 49697.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.036129 restraints weight = 40060.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2733 r_free = 0.2733 target = 0.036148 restraints weight = 35499.678| |-----------------------------------------------------------------------------| r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2715 r_free = 0.2715 target_work(ls_wunit_k1) = 0.036 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2715 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.083 20446 Z= 0.296 Angle : 0.671 11.499 27871 Z= 0.356 Chirality : 0.051 0.304 3133 Planarity : 0.005 0.059 3604 Dihedral : 5.363 34.126 2786 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.26 (0.16), residues: 2557 helix: -0.14 (0.41), residues: 159 sheet: -0.26 (0.19), residues: 776 loop : -1.23 (0.14), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG c 891 TYR 0.033 0.002 TYR e 19 PHE 0.020 0.002 PHE e 485 TRP 0.018 0.002 TRP d 946 HIS 0.009 0.002 HIS e 26 Details of bonding type rmsd covalent geometry : bond 0.00667 (20446) covalent geometry : angle 0.67100 (27871) hydrogen bonds : bond 0.03555 ( 451) hydrogen bonds : angle 6.78654 ( 1173) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 778 HIS cc_start: 0.5796 (t-170) cc_final: 0.5536 (t-170) REVERT: d 798 MET cc_start: 0.3328 (ptt) cc_final: 0.3055 (ptt) REVERT: d 892 MET cc_start: 0.8519 (tmm) cc_final: 0.7791 (tmm) REVERT: b 788 GLN cc_start: 0.6549 (tm-30) cc_final: 0.6092 (tm-30) REVERT: e 430 MET cc_start: 0.7928 (ttm) cc_final: 0.7521 (tmm) REVERT: g 456 ILE cc_start: 0.8757 (tt) cc_final: 0.8535 (mt) REVERT: c 742 PHE cc_start: 0.7240 (t80) cc_final: 0.6887 (t80) REVERT: c 892 MET cc_start: 0.8489 (tpt) cc_final: 0.8234 (tpt) REVERT: c 915 PHE cc_start: 0.7630 (m-10) cc_final: 0.6746 (m-10) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.1199 time to fit residues: 17.4180 Evaluate side-chains 67 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 244 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 171 optimal weight: 0.8980 chunk 210 optimal weight: 0.9980 chunk 196 optimal weight: 2.9990 chunk 249 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 162 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 469 ASN ** f 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN g 411 ASN g 686 HIS ** c 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 919 ASN ** c 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.046117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.036273 restraints weight = 122171.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.037082 restraints weight = 68580.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.037659 restraints weight = 45404.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.038000 restraints weight = 33756.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.038214 restraints weight = 27765.214| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20446 Z= 0.115 Angle : 0.553 9.861 27871 Z= 0.293 Chirality : 0.049 0.335 3133 Planarity : 0.004 0.055 3604 Dihedral : 4.843 34.520 2786 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.05 % Allowed : 0.69 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.91 (0.16), residues: 2557 helix: 0.44 (0.45), residues: 153 sheet: -0.12 (0.18), residues: 819 loop : -0.98 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG f 206 TYR 0.019 0.001 TYR f 487 PHE 0.013 0.001 PHE g 327 TRP 0.014 0.001 TRP d 946 HIS 0.005 0.001 HIS d 778 Details of bonding type rmsd covalent geometry : bond 0.00260 (20446) covalent geometry : angle 0.55275 (27871) hydrogen bonds : bond 0.03005 ( 451) hydrogen bonds : angle 6.47876 ( 1173) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 91 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 778 HIS cc_start: 0.5937 (t-170) cc_final: 0.5712 (t-170) REVERT: d 890 ASP cc_start: 0.7794 (t0) cc_final: 0.7174 (p0) REVERT: d 892 MET cc_start: 0.8298 (tmm) cc_final: 0.7972 (tmm) REVERT: b 788 GLN cc_start: 0.6618 (tm-30) cc_final: 0.6184 (tm-30) REVERT: b 798 MET cc_start: 0.5950 (ptt) cc_final: 0.5728 (ppp) REVERT: f 507 TRP cc_start: 0.5728 (m-10) cc_final: 0.5049 (m-10) REVERT: f 676 MET cc_start: 0.8124 (ttp) cc_final: 0.7881 (ttp) REVERT: e 430 MET cc_start: 0.7893 (ttm) cc_final: 0.7449 (tmm) REVERT: e 432 MET cc_start: 0.7919 (mmm) cc_final: 0.7700 (mtt) REVERT: c 742 PHE cc_start: 0.7137 (t80) cc_final: 0.6896 (t80) REVERT: c 915 PHE cc_start: 0.7303 (m-10) cc_final: 0.7016 (m-10) outliers start: 1 outliers final: 0 residues processed: 92 average time/residue: 0.1171 time to fit residues: 18.4280 Evaluate side-chains 70 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 23 optimal weight: 30.0000 chunk 222 optimal weight: 2.9990 chunk 210 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 117 optimal weight: 0.6980 chunk 88 optimal weight: 6.9990 chunk 209 optimal weight: 3.9990 chunk 195 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 213 optimal weight: 0.9980 chunk 177 optimal weight: 0.3980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN g 148 ASN g 411 ASN ** c 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.045969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.037016 restraints weight = 123244.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.037558 restraints weight = 69833.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.037881 restraints weight = 46605.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.038065 restraints weight = 38101.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.038071 restraints weight = 34047.587| |-----------------------------------------------------------------------------| r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.038 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 20446 Z= 0.121 Angle : 0.551 10.150 27871 Z= 0.289 Chirality : 0.049 0.334 3133 Planarity : 0.004 0.054 3604 Dihedral : 4.752 37.647 2786 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.05 % Allowed : 0.32 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.80 (0.16), residues: 2557 helix: 0.48 (0.45), residues: 154 sheet: -0.06 (0.18), residues: 822 loop : -0.90 (0.15), residues: 1581 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG c 894 TYR 0.051 0.001 TYR e 487 PHE 0.014 0.001 PHE f 586 TRP 0.055 0.001 TRP e 507 HIS 0.004 0.001 HIS d 778 Details of bonding type rmsd covalent geometry : bond 0.00277 (20446) covalent geometry : angle 0.55110 (27871) hydrogen bonds : bond 0.02939 ( 451) hydrogen bonds : angle 6.30802 ( 1173) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5114 Ramachandran restraints generated. 2557 Oldfield, 0 Emsley, 2557 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 95 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: d 778 HIS cc_start: 0.6004 (t-170) cc_final: 0.5733 (t-170) REVERT: d 798 MET cc_start: 0.3236 (ptt) cc_final: 0.3002 (ptt) REVERT: d 890 ASP cc_start: 0.7907 (t0) cc_final: 0.7289 (p0) REVERT: d 892 MET cc_start: 0.8398 (tmm) cc_final: 0.7988 (tmm) REVERT: b 743 LYS cc_start: 0.8594 (tptm) cc_final: 0.8370 (tppt) REVERT: f 507 TRP cc_start: 0.5811 (m-10) cc_final: 0.5011 (m-10) REVERT: f 676 MET cc_start: 0.8053 (ttp) cc_final: 0.7812 (ttp) REVERT: e 430 MET cc_start: 0.7776 (ttm) cc_final: 0.7453 (tmm) REVERT: c 742 PHE cc_start: 0.7105 (t80) cc_final: 0.6849 (t80) REVERT: c 915 PHE cc_start: 0.7266 (m-10) cc_final: 0.6975 (m-10) outliers start: 1 outliers final: 0 residues processed: 96 average time/residue: 0.1174 time to fit residues: 19.5654 Evaluate side-chains 75 residues out of total 2176 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 152 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 174 optimal weight: 0.8980 chunk 79 optimal weight: 8.9990 chunk 141 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 195 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 194 optimal weight: 0.4980 chunk 240 optimal weight: 8.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 636 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 273 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 479 GLN g 411 ASN ** c 889 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 939 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.045759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.036781 restraints weight = 123707.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2777 r_free = 0.2777 target = 0.037341 restraints weight = 69578.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.037635 restraints weight = 45727.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.037799 restraints weight = 39281.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.037787 restraints weight = 35049.013| |-----------------------------------------------------------------------------| r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.037 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20446 Z= 0.141 Angle : 0.545 10.539 27871 Z= 0.286 Chirality : 0.048 0.326 3133 Planarity : 0.004 0.053 3604 Dihedral : 4.736 37.362 2786 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.05 % Allowed : 0.41 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.84 (0.16), residues: 2557 helix: 0.51 (0.44), residues: 159 sheet: -0.12 (0.18), residues: 836 loop : -0.91 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG c 891 TYR 0.023 0.001 TYR e 487 PHE 0.015 0.001 PHE e 485 TRP 0.011 0.001 TRP d 946 HIS 0.003 0.001 HIS e 26 Details of bonding type rmsd covalent geometry : bond 0.00323 (20446) covalent geometry : angle 0.54524 (27871) hydrogen bonds : bond 0.02947 ( 451) hydrogen bonds : angle 6.26878 ( 1173) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2538.79 seconds wall clock time: 45 minutes 13.27 seconds (2713.27 seconds total)