Starting phenix.real_space_refine on Sun Aug 24 18:34:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i6p_35202/08_2025/8i6p_35202.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i6p_35202/08_2025/8i6p_35202.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8i6p_35202/08_2025/8i6p_35202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i6p_35202/08_2025/8i6p_35202.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8i6p_35202/08_2025/8i6p_35202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i6p_35202/08_2025/8i6p_35202.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 140 5.16 5 C 13968 2.51 5 N 3776 2.21 5 O 4132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 164 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22016 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5504 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Chain: "C" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5504 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Chain: "D" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5504 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Chain: "A" Number of atoms: 5504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5504 Classifications: {'peptide': 688} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 662} Time building chain proxies: 5.28, per 1000 atoms: 0.24 Number of scatterers: 22016 At special positions: 0 Unit cell: (180.83, 131.61, 141.24, 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 140 16.00 O 4132 8.00 N 3776 7.00 C 13968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 895.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5144 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 8 sheets defined 69.4% alpha, 0.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'B' and resid 80 through 93 removed outlier: 4.148A pdb=" N ILE B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 112 removed outlier: 3.504A pdb=" N LEU B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 Processing helix chain 'B' and resid 147 through 165 removed outlier: 3.814A pdb=" N MET B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 183 removed outlier: 3.805A pdb=" N CYS B 172 " --> pdb=" O HIS B 168 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU B 177 " --> pdb=" O GLU B 173 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE B 178 " --> pdb=" O ARG B 174 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 189 removed outlier: 3.527A pdb=" N ALA B 187 " --> pdb=" O TRP B 184 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU B 189 " --> pdb=" O LEU B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 213 Proline residue: B 203 - end of helix removed outlier: 3.709A pdb=" N ASP B 211 " --> pdb=" O ASP B 207 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU B 212 " --> pdb=" O MET B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 237 Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 247 through 252 Processing helix chain 'B' and resid 277 through 286 removed outlier: 3.562A pdb=" N THR B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 303 removed outlier: 3.546A pdb=" N PHE B 294 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR B 296 " --> pdb=" O LYS B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 329 removed outlier: 3.579A pdb=" N VAL B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG B 325 " --> pdb=" O TRP B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 349 Processing helix chain 'B' and resid 365 through 378 removed outlier: 3.899A pdb=" N THR B 369 " --> pdb=" O ASP B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 390 removed outlier: 4.166A pdb=" N VAL B 387 " --> pdb=" O ASP B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 419 removed outlier: 4.502A pdb=" N MET B 412 " --> pdb=" O SER B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 446 removed outlier: 3.828A pdb=" N ASP B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY B 446 " --> pdb=" O GLN B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 470 removed outlier: 4.330A pdb=" N GLU B 463 " --> pdb=" O ASP B 459 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 475 Processing helix chain 'B' and resid 476 through 485 Processing helix chain 'B' and resid 509 through 540 removed outlier: 3.601A pdb=" N LYS B 513 " --> pdb=" O ASP B 509 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL B 528 " --> pdb=" O LYS B 524 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN B 531 " --> pdb=" O ARG B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 541 through 546 Processing helix chain 'B' and resid 549 through 565 removed outlier: 3.986A pdb=" N THR B 553 " --> pdb=" O ASP B 549 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN B 564 " --> pdb=" O LEU B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 570 through 595 Processing helix chain 'B' and resid 596 through 600 Processing helix chain 'B' and resid 603 through 611 removed outlier: 4.441A pdb=" N ILE B 608 " --> pdb=" O GLU B 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 617 through 635 removed outlier: 4.024A pdb=" N LEU B 621 " --> pdb=" O TYR B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 659 Processing helix chain 'B' and resid 666 through 696 removed outlier: 3.759A pdb=" N LEU B 670 " --> pdb=" O GLN B 666 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN B 696 " --> pdb=" O LEU B 692 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 722 removed outlier: 3.765A pdb=" N VAL B 703 " --> pdb=" O SER B 699 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU B 713 " --> pdb=" O GLN B 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 747 removed outlier: 4.219A pdb=" N PHE B 736 " --> pdb=" O THR B 732 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU B 737 " --> pdb=" O ARG B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 763 removed outlier: 4.036A pdb=" N SER B 756 " --> pdb=" O GLU B 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 93 removed outlier: 3.503A pdb=" N SER C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 112 removed outlier: 3.504A pdb=" N LEU C 108 " --> pdb=" O TYR C 104 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 133 Processing helix chain 'C' and resid 147 through 165 removed outlier: 3.813A pdb=" N MET C 153 " --> pdb=" O GLY C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 183 removed outlier: 3.805A pdb=" N CYS C 172 " --> pdb=" O HIS C 168 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU C 177 " --> pdb=" O GLU C 173 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE C 178 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 189 removed outlier: 3.526A pdb=" N ALA C 187 " --> pdb=" O TRP C 184 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU C 189 " --> pdb=" O LEU C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 213 Proline residue: C 203 - end of helix removed outlier: 3.709A pdb=" N ASP C 211 " --> pdb=" O ASP C 207 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU C 212 " --> pdb=" O MET C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 237 Processing helix chain 'C' and resid 239 through 245 Processing helix chain 'C' and resid 247 through 252 Processing helix chain 'C' and resid 277 through 286 removed outlier: 3.562A pdb=" N THR C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 303 removed outlier: 3.547A pdb=" N PHE C 294 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR C 296 " --> pdb=" O LYS C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 329 removed outlier: 3.578A pdb=" N VAL C 323 " --> pdb=" O ARG C 319 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG C 325 " --> pdb=" O TRP C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 349 Processing helix chain 'C' and resid 365 through 378 removed outlier: 3.899A pdb=" N THR C 369 " --> pdb=" O ASP C 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 390 removed outlier: 4.166A pdb=" N VAL C 387 " --> pdb=" O ASP C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 408 through 419 removed outlier: 4.503A pdb=" N MET C 412 " --> pdb=" O SER C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 446 removed outlier: 3.828A pdb=" N ASP C 443 " --> pdb=" O SER C 439 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG C 444 " --> pdb=" O PHE C 440 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY C 446 " --> pdb=" O GLN C 442 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 470 removed outlier: 4.330A pdb=" N GLU C 463 " --> pdb=" O ASP C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 471 through 475 Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 509 through 540 removed outlier: 3.601A pdb=" N LYS C 513 " --> pdb=" O ASP C 509 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL C 528 " --> pdb=" O LYS C 524 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN C 531 " --> pdb=" O ARG C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 546 Processing helix chain 'C' and resid 549 through 565 removed outlier: 3.986A pdb=" N THR C 553 " --> pdb=" O ASP C 549 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN C 564 " --> pdb=" O LEU C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 569 No H-bonds generated for 'chain 'C' and resid 567 through 569' Processing helix chain 'C' and resid 570 through 595 Processing helix chain 'C' and resid 596 through 600 Processing helix chain 'C' and resid 603 through 611 removed outlier: 4.441A pdb=" N ILE C 608 " --> pdb=" O GLU C 605 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 635 removed outlier: 4.025A pdb=" N LEU C 621 " --> pdb=" O TYR C 617 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 659 Processing helix chain 'C' and resid 666 through 696 removed outlier: 3.760A pdb=" N LEU C 670 " --> pdb=" O GLN C 666 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN C 696 " --> pdb=" O LEU C 692 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 722 removed outlier: 3.765A pdb=" N VAL C 703 " --> pdb=" O SER C 699 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU C 713 " --> pdb=" O GLN C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 747 removed outlier: 4.219A pdb=" N PHE C 736 " --> pdb=" O THR C 732 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 737 " --> pdb=" O ARG C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 750 through 763 removed outlier: 4.035A pdb=" N SER C 756 " --> pdb=" O GLU C 752 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 93 removed outlier: 3.504A pdb=" N SER D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 112 removed outlier: 3.505A pdb=" N LEU D 108 " --> pdb=" O TYR D 104 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 112 " --> pdb=" O LEU D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 133 Processing helix chain 'D' and resid 147 through 165 removed outlier: 3.813A pdb=" N MET D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 183 removed outlier: 3.806A pdb=" N CYS D 172 " --> pdb=" O HIS D 168 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 177 " --> pdb=" O GLU D 173 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE D 178 " --> pdb=" O ARG D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 removed outlier: 3.526A pdb=" N ALA D 187 " --> pdb=" O TRP D 184 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU D 189 " --> pdb=" O LEU D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 213 Proline residue: D 203 - end of helix removed outlier: 3.708A pdb=" N ASP D 211 " --> pdb=" O ASP D 207 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU D 212 " --> pdb=" O MET D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 237 Processing helix chain 'D' and resid 239 through 245 Processing helix chain 'D' and resid 247 through 252 Processing helix chain 'D' and resid 277 through 286 removed outlier: 3.562A pdb=" N THR D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 303 removed outlier: 3.547A pdb=" N PHE D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR D 296 " --> pdb=" O LYS D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 329 removed outlier: 3.579A pdb=" N VAL D 323 " --> pdb=" O ARG D 319 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG D 325 " --> pdb=" O TRP D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 349 Processing helix chain 'D' and resid 365 through 378 removed outlier: 3.899A pdb=" N THR D 369 " --> pdb=" O ASP D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 390 removed outlier: 4.165A pdb=" N VAL D 387 " --> pdb=" O ASP D 384 " (cutoff:3.500A) Processing helix chain 'D' and resid 408 through 419 removed outlier: 4.502A pdb=" N MET D 412 " --> pdb=" O SER D 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 446 removed outlier: 3.828A pdb=" N ASP D 443 " --> pdb=" O SER D 439 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ARG D 444 " --> pdb=" O PHE D 440 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY D 446 " --> pdb=" O GLN D 442 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 470 removed outlier: 4.329A pdb=" N GLU D 463 " --> pdb=" O ASP D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 471 through 475 Processing helix chain 'D' and resid 476 through 485 Processing helix chain 'D' and resid 509 through 540 removed outlier: 3.601A pdb=" N LYS D 513 " --> pdb=" O ASP D 509 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL D 528 " --> pdb=" O LYS D 524 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASN D 531 " --> pdb=" O ARG D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 546 Processing helix chain 'D' and resid 549 through 565 removed outlier: 3.987A pdb=" N THR D 553 " --> pdb=" O ASP D 549 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASN D 564 " --> pdb=" O LEU D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 567 through 569 No H-bonds generated for 'chain 'D' and resid 567 through 569' Processing helix chain 'D' and resid 570 through 595 Processing helix chain 'D' and resid 596 through 600 Processing helix chain 'D' and resid 603 through 611 removed outlier: 4.442A pdb=" N ILE D 608 " --> pdb=" O GLU D 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 617 through 635 removed outlier: 4.024A pdb=" N LEU D 621 " --> pdb=" O TYR D 617 " (cutoff:3.500A) Processing helix chain 'D' and resid 643 through 659 Processing helix chain 'D' and resid 666 through 696 removed outlier: 3.760A pdb=" N LEU D 670 " --> pdb=" O GLN D 666 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASN D 696 " --> pdb=" O LEU D 692 " (cutoff:3.500A) Processing helix chain 'D' and resid 699 through 722 removed outlier: 3.764A pdb=" N VAL D 703 " --> pdb=" O SER D 699 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU D 713 " --> pdb=" O GLN D 709 " (cutoff:3.500A) Processing helix chain 'D' and resid 730 through 747 removed outlier: 4.218A pdb=" N PHE D 736 " --> pdb=" O THR D 732 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU D 737 " --> pdb=" O ARG D 733 " (cutoff:3.500A) Processing helix chain 'D' and resid 750 through 763 removed outlier: 4.034A pdb=" N SER D 756 " --> pdb=" O GLU D 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 93 removed outlier: 3.504A pdb=" N SER A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 112 removed outlier: 3.505A pdb=" N LEU A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 133 Processing helix chain 'A' and resid 147 through 165 removed outlier: 3.813A pdb=" N MET A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 183 removed outlier: 3.805A pdb=" N CYS A 172 " --> pdb=" O HIS A 168 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE A 178 " --> pdb=" O ARG A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 removed outlier: 3.526A pdb=" N ALA A 187 " --> pdb=" O TRP A 184 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 189 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 213 Proline residue: A 203 - end of helix removed outlier: 3.709A pdb=" N ASP A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU A 212 " --> pdb=" O MET A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 237 Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 247 through 252 Processing helix chain 'A' and resid 277 through 286 removed outlier: 3.561A pdb=" N THR A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 303 removed outlier: 3.547A pdb=" N PHE A 294 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 296 " --> pdb=" O LYS A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 329 removed outlier: 3.579A pdb=" N VAL A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG A 325 " --> pdb=" O TRP A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 349 Processing helix chain 'A' and resid 365 through 378 removed outlier: 3.900A pdb=" N THR A 369 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 390 removed outlier: 4.165A pdb=" N VAL A 387 " --> pdb=" O ASP A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 419 removed outlier: 4.503A pdb=" N MET A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 446 removed outlier: 3.828A pdb=" N ASP A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY A 446 " --> pdb=" O GLN A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 470 removed outlier: 4.329A pdb=" N GLU A 463 " --> pdb=" O ASP A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 509 through 540 removed outlier: 3.602A pdb=" N LYS A 513 " --> pdb=" O ASP A 509 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 528 " --> pdb=" O LYS A 524 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 531 " --> pdb=" O ARG A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 546 Processing helix chain 'A' and resid 549 through 565 removed outlier: 3.986A pdb=" N THR A 553 " --> pdb=" O ASP A 549 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN A 564 " --> pdb=" O LEU A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 570 through 595 Processing helix chain 'A' and resid 596 through 600 Processing helix chain 'A' and resid 603 through 611 removed outlier: 4.441A pdb=" N ILE A 608 " --> pdb=" O GLU A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 617 through 635 removed outlier: 4.025A pdb=" N LEU A 621 " --> pdb=" O TYR A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 659 Processing helix chain 'A' and resid 666 through 696 removed outlier: 3.760A pdb=" N LEU A 670 " --> pdb=" O GLN A 666 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN A 696 " --> pdb=" O LEU A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 722 removed outlier: 3.765A pdb=" N VAL A 703 " --> pdb=" O SER A 699 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU A 713 " --> pdb=" O GLN A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 747 removed outlier: 4.219A pdb=" N PHE A 736 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LEU A 737 " --> pdb=" O ARG A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 763 removed outlier: 4.035A pdb=" N SER A 756 " --> pdb=" O GLU A 752 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 392 through 393 Processing sheet with id=AA2, first strand: chain 'B' and resid 455 through 456 Processing sheet with id=AA3, first strand: chain 'C' and resid 392 through 393 Processing sheet with id=AA4, first strand: chain 'C' and resid 455 through 456 Processing sheet with id=AA5, first strand: chain 'D' and resid 392 through 393 Processing sheet with id=AA6, first strand: chain 'D' and resid 455 through 456 Processing sheet with id=AA7, first strand: chain 'A' and resid 392 through 393 Processing sheet with id=AA8, first strand: chain 'A' and resid 455 through 456 1252 hydrogen bonds defined for protein. 3504 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: 3.65 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7271 1.35 - 1.47: 5371 1.47 - 1.59: 9658 1.59 - 1.71: 0 1.71 - 1.83: 208 Bond restraints: 22508 Sorted by residual: bond pdb=" C LYS D 422 " pdb=" N PHE D 423 " ideal model delta sigma weight residual 1.331 1.244 0.087 2.07e-02 2.33e+03 1.75e+01 bond pdb=" C LYS C 422 " pdb=" N PHE C 423 " ideal model delta sigma weight residual 1.331 1.245 0.086 2.07e-02 2.33e+03 1.73e+01 bond pdb=" C LYS B 422 " pdb=" N PHE B 423 " ideal model delta sigma weight residual 1.331 1.245 0.086 2.07e-02 2.33e+03 1.72e+01 bond pdb=" C LYS A 422 " pdb=" N PHE A 423 " ideal model delta sigma weight residual 1.331 1.245 0.086 2.07e-02 2.33e+03 1.72e+01 bond pdb=" N VAL D 301 " pdb=" CA VAL D 301 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.22e-02 6.72e+03 8.77e+00 ... (remaining 22503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.62: 30093 2.62 - 5.23: 321 5.23 - 7.85: 34 7.85 - 10.46: 4 10.46 - 13.08: 8 Bond angle restraints: 30460 Sorted by residual: angle pdb=" CA GLU B 340 " pdb=" CB GLU B 340 " pdb=" CG GLU B 340 " ideal model delta sigma weight residual 114.10 125.10 -11.00 2.00e+00 2.50e-01 3.02e+01 angle pdb=" CA GLU A 340 " pdb=" CB GLU A 340 " pdb=" CG GLU A 340 " ideal model delta sigma weight residual 114.10 125.08 -10.98 2.00e+00 2.50e-01 3.01e+01 angle pdb=" CA GLU C 340 " pdb=" CB GLU C 340 " pdb=" CG GLU C 340 " ideal model delta sigma weight residual 114.10 125.08 -10.98 2.00e+00 2.50e-01 3.01e+01 angle pdb=" CA GLU D 340 " pdb=" CB GLU D 340 " pdb=" CG GLU D 340 " ideal model delta sigma weight residual 114.10 125.06 -10.96 2.00e+00 2.50e-01 3.00e+01 angle pdb=" CB MET C 245 " pdb=" CG MET C 245 " pdb=" SD MET C 245 " ideal model delta sigma weight residual 112.70 125.78 -13.08 3.00e+00 1.11e-01 1.90e+01 ... (remaining 30455 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 11553 17.68 - 35.36: 1220 35.36 - 53.05: 502 53.05 - 70.73: 141 70.73 - 88.41: 60 Dihedral angle restraints: 13476 sinusoidal: 5496 harmonic: 7980 Sorted by residual: dihedral pdb=" CA LYS B 544 " pdb=" C LYS B 544 " pdb=" N PHE B 545 " pdb=" CA PHE B 545 " ideal model delta harmonic sigma weight residual 180.00 160.29 19.71 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LYS D 544 " pdb=" C LYS D 544 " pdb=" N PHE D 545 " pdb=" CA PHE D 545 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LYS C 544 " pdb=" C LYS C 544 " pdb=" N PHE C 545 " pdb=" CA PHE C 545 " ideal model delta harmonic sigma weight residual 180.00 160.32 19.68 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 13473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2209 0.038 - 0.076: 838 0.076 - 0.114: 226 0.114 - 0.152: 34 0.152 - 0.190: 9 Chirality restraints: 3316 Sorted by residual: chirality pdb=" CA GLU D 340 " pdb=" N GLU D 340 " pdb=" C GLU D 340 " pdb=" CB GLU D 340 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CA GLU A 340 " pdb=" N GLU A 340 " pdb=" C GLU A 340 " pdb=" CB GLU A 340 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" CA GLU C 340 " pdb=" N GLU C 340 " pdb=" C GLU C 340 " pdb=" CB GLU C 340 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.70e-01 ... (remaining 3313 not shown) Planarity restraints: 3920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 384 " 0.034 5.00e-02 4.00e+02 5.13e-02 4.22e+00 pdb=" N PRO B 385 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO B 385 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 385 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 384 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO A 385 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 385 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 385 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 384 " 0.034 5.00e-02 4.00e+02 5.12e-02 4.19e+00 pdb=" N PRO D 385 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 385 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 385 " 0.028 5.00e-02 4.00e+02 ... (remaining 3917 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 360 2.53 - 3.12: 19673 3.12 - 3.72: 37344 3.72 - 4.31: 48261 4.31 - 4.90: 77085 Nonbonded interactions: 182723 Sorted by model distance: nonbonded pdb=" O LEU D 297 " pdb=" CG1 VAL D 301 " model vdw 1.938 3.460 nonbonded pdb=" OD1 ASP A 365 " pdb=" N ILE A 366 " model vdw 2.088 3.120 nonbonded pdb=" OD1 ASP C 365 " pdb=" N ILE C 366 " model vdw 2.088 3.120 nonbonded pdb=" OD1 ASP D 365 " pdb=" N ILE D 366 " model vdw 2.088 3.120 nonbonded pdb=" OD1 ASP B 365 " pdb=" N ILE B 366 " model vdw 2.089 3.120 ... (remaining 182718 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.06 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'A' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 20.440 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 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 : 0.005 0.087 22508 Z= 0.279 Angle : 0.760 13.075 30460 Z= 0.440 Chirality : 0.043 0.190 3316 Planarity : 0.004 0.051 3920 Dihedral : 18.817 88.412 8332 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 21.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 15.58 % Allowed : 18.09 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 aren not related in a simple way. whole: -3.57 (0.13), residues: 2744 helix: -2.03 (0.10), residues: 1724 sheet: None (None), residues: 0 loop : -2.78 (0.16), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 593 TYR 0.012 0.001 TYR A 466 PHE 0.009 0.001 PHE D 294 TRP 0.011 0.002 TRP C 321 HIS 0.004 0.001 HIS D 334 Details of bonding type rmsd covalent geometry : bond 0.00547 (22508) covalent geometry : angle 0.76003 (30460) hydrogen bonds : bond 0.13418 ( 1252) hydrogen bonds : angle 5.81048 ( 3504) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 372 poor density : 216 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 SER cc_start: 0.5129 (OUTLIER) cc_final: 0.4719 (p) REVERT: B 146 PHE cc_start: 0.6287 (t80) cc_final: 0.5938 (t80) REVERT: B 148 MET cc_start: 0.6829 (OUTLIER) cc_final: 0.6360 (mmm) REVERT: B 183 MET cc_start: 0.8390 (mmm) cc_final: 0.7894 (tpp) REVERT: B 194 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7422 (mmm) REVERT: B 450 MET cc_start: 0.6141 (mmt) cc_final: 0.5757 (mmt) REVERT: B 459 ASP cc_start: 0.5463 (OUTLIER) cc_final: 0.5227 (p0) REVERT: B 541 ASN cc_start: 0.7438 (t0) cc_final: 0.7171 (t0) REVERT: B 555 MET cc_start: 0.8121 (tpp) cc_final: 0.7858 (mmm) REVERT: B 569 ASN cc_start: 0.7670 (OUTLIER) cc_final: 0.7237 (p0) REVERT: B 607 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8151 (tt) REVERT: B 610 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8122 (mt) REVERT: B 622 ARG cc_start: 0.7389 (mtm110) cc_final: 0.7068 (mtp85) REVERT: B 725 CYS cc_start: 0.6039 (OUTLIER) cc_final: 0.5326 (m) REVERT: C 100 SER cc_start: 0.5323 (OUTLIER) cc_final: 0.4790 (p) REVERT: C 148 MET cc_start: 0.6799 (OUTLIER) cc_final: 0.6437 (mmt) REVERT: C 153 MET cc_start: 0.8212 (mtp) cc_final: 0.7979 (mmm) REVERT: C 183 MET cc_start: 0.8429 (mmm) cc_final: 0.7648 (ppp) REVERT: C 191 GLU cc_start: 0.6556 (OUTLIER) cc_final: 0.5263 (tm-30) REVERT: C 240 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8195 (p0) REVERT: C 256 MET cc_start: 0.7292 (mmm) cc_final: 0.6559 (tmm) REVERT: C 257 VAL cc_start: 0.5695 (OUTLIER) cc_final: 0.5447 (t) REVERT: C 378 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8895 (tp) REVERT: C 400 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7356 (tt) REVERT: C 450 MET cc_start: 0.6383 (mmt) cc_final: 0.5842 (mmt) REVERT: C 459 ASP cc_start: 0.5766 (OUTLIER) cc_final: 0.5451 (t0) REVERT: C 480 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7607 (mt-10) REVERT: C 607 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8195 (tt) REVERT: C 725 CYS cc_start: 0.5780 (OUTLIER) cc_final: 0.4695 (m) REVERT: C 734 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: D 123 PHE cc_start: 0.7657 (m-80) cc_final: 0.7082 (m-80) REVERT: D 125 SER cc_start: 0.7884 (OUTLIER) cc_final: 0.7607 (m) REVERT: D 240 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7589 (t0) REVERT: D 245 MET cc_start: 0.7444 (OUTLIER) cc_final: 0.7136 (mmm) REVERT: D 257 VAL cc_start: 0.6272 (OUTLIER) cc_final: 0.5291 (m) REVERT: D 271 ASP cc_start: 0.6899 (OUTLIER) cc_final: 0.6609 (t70) REVERT: D 293 CYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7240 (t) REVERT: D 321 TRP cc_start: 0.7886 (m100) cc_final: 0.7518 (m100) REVERT: D 353 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.6796 (t70) REVERT: D 366 ILE cc_start: 0.8616 (tt) cc_final: 0.8410 (tp) REVERT: D 412 MET cc_start: 0.8023 (mtt) cc_final: 0.7787 (mmm) REVERT: D 569 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7528 (p0) REVERT: D 684 CYS cc_start: 0.7670 (m) cc_final: 0.7131 (m) REVERT: D 734 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7285 (pt0) REVERT: A 125 SER cc_start: 0.7557 (OUTLIER) cc_final: 0.7352 (m) REVERT: A 240 ASP cc_start: 0.8055 (OUTLIER) cc_final: 0.7633 (m-30) REVERT: A 266 LYS cc_start: 0.8688 (OUTLIER) cc_final: 0.8403 (ptpp) REVERT: A 321 TRP cc_start: 0.7961 (m100) cc_final: 0.7454 (m100) REVERT: A 353 ASP cc_start: 0.7880 (OUTLIER) cc_final: 0.7554 (t70) REVERT: A 360 ASN cc_start: 0.7045 (OUTLIER) cc_final: 0.6214 (p0) REVERT: A 569 ASN cc_start: 0.7885 (OUTLIER) cc_final: 0.7614 (p0) REVERT: A 695 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6945 (mp0) outliers start: 372 outliers final: 107 residues processed: 543 average time/residue: 0.1399 time to fit residues: 120.5133 Evaluate side-chains 253 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 111 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 100 SER Chi-restraints excluded: chain B residue 111 LEU Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 148 MET Chi-restraints excluded: chain B residue 194 MET Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 353 ASP Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 459 ASP Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain B residue 520 SER Chi-restraints excluded: chain B residue 540 SER Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain B residue 569 ASN Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 605 GLU Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 609 SER Chi-restraints excluded: chain B residue 610 LEU Chi-restraints excluded: chain B residue 645 ASP Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 685 CYS Chi-restraints excluded: chain B residue 725 CYS Chi-restraints excluded: chain B residue 734 GLU Chi-restraints excluded: chain B residue 740 VAL Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain C residue 93 SER Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 128 ASP Chi-restraints excluded: chain C residue 148 MET Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 194 MET Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 257 VAL Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 399 CYS Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 459 ASP Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain C residue 520 SER Chi-restraints excluded: chain C residue 540 SER Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 605 GLU Chi-restraints excluded: chain C residue 607 LEU Chi-restraints excluded: chain C residue 609 SER Chi-restraints excluded: chain C residue 635 LYS Chi-restraints excluded: chain C residue 645 ASP Chi-restraints excluded: chain C residue 651 VAL Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 670 LEU Chi-restraints excluded: chain C residue 695 GLU Chi-restraints excluded: chain C residue 721 VAL Chi-restraints excluded: chain C residue 725 CYS Chi-restraints excluded: chain C residue 734 GLU Chi-restraints excluded: chain C residue 739 VAL Chi-restraints excluded: chain C residue 740 VAL Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 128 ASP Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 271 ASP Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 293 CYS Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 332 SER Chi-restraints excluded: chain D residue 340 GLU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 399 CYS Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 569 ASN Chi-restraints excluded: chain D residue 580 VAL Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 605 GLU Chi-restraints excluded: chain D residue 645 ASP Chi-restraints excluded: chain D residue 651 VAL Chi-restraints excluded: chain D residue 662 VAL Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 670 LEU Chi-restraints excluded: chain D residue 674 SER Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 685 CYS Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 695 GLU Chi-restraints excluded: chain D residue 734 GLU Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 128 ASP Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 332 SER Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 360 ASN Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 569 ASN Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 651 VAL Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 695 GLU Chi-restraints excluded: chain A residue 710 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.0670 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 10.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.2980 chunk 111 optimal weight: 7.9990 overall best weight: 2.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 357 HIS B 414 ASN B 442 GLN B 531 ASN B 590 HIS B 678 GLN B 709 GLN B 764 GLN C 414 ASN C 531 ASN C 551 GLN C 590 HIS C 678 GLN C 709 GLN C 764 GLN D 166 ASN D 334 HIS D 357 HIS D 531 ASN D 551 GLN D 590 HIS D 709 GLN D 757 HIS D 764 GLN A 291 GLN A 357 HIS A 405 ASN A 531 ASN A 551 GLN A 590 HIS A 709 GLN A 757 HIS A 764 GLN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.041221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.034611 restraints weight = 233377.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.035515 restraints weight = 121015.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.036111 restraints weight = 77559.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.036515 restraints weight = 56587.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.036785 restraints weight = 45206.918| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22508 Z= 0.134 Angle : 0.598 9.932 30460 Z= 0.308 Chirality : 0.041 0.164 3316 Planarity : 0.004 0.046 3920 Dihedral : 9.078 125.683 3246 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 5.61 % Allowed : 20.69 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 aren not related in a simple way. whole: -1.29 (0.15), residues: 2744 helix: 0.01 (0.12), residues: 1728 sheet: None (None), residues: 0 loop : -2.37 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 593 TYR 0.015 0.001 TYR A 413 PHE 0.015 0.001 PHE D 398 TRP 0.018 0.002 TRP D 129 HIS 0.004 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00284 (22508) covalent geometry : angle 0.59836 (30460) hydrogen bonds : bond 0.04682 ( 1252) hydrogen bonds : angle 4.26337 ( 3504) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 129 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 MET cc_start: 0.8320 (mmm) cc_final: 0.7545 (tpp) REVERT: B 194 MET cc_start: 0.7872 (mmt) cc_final: 0.7588 (tpp) REVERT: B 419 SER cc_start: 0.8195 (OUTLIER) cc_final: 0.7893 (t) REVERT: B 450 MET cc_start: 0.6148 (mmt) cc_final: 0.5911 (mmt) REVERT: B 480 GLU cc_start: 0.8112 (tt0) cc_final: 0.7819 (mt-10) REVERT: B 607 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8091 (tp) REVERT: C 183 MET cc_start: 0.8239 (mmm) cc_final: 0.7792 (ppp) REVERT: C 240 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8142 (p0) REVERT: C 256 MET cc_start: 0.7147 (mmm) cc_final: 0.6637 (tmm) REVERT: C 340 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: C 476 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7730 (mt) REVERT: C 480 GLU cc_start: 0.8066 (tt0) cc_final: 0.7618 (mt-10) REVERT: D 123 PHE cc_start: 0.7892 (m-80) cc_final: 0.7308 (m-80) REVERT: D 125 SER cc_start: 0.7894 (OUTLIER) cc_final: 0.7576 (m) REVERT: D 240 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7521 (p0) REVERT: D 245 MET cc_start: 0.7771 (OUTLIER) cc_final: 0.7538 (mmm) REVERT: D 257 VAL cc_start: 0.5689 (OUTLIER) cc_final: 0.5489 (m) REVERT: D 321 TRP cc_start: 0.7853 (m100) cc_final: 0.7582 (m100) REVERT: D 605 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7325 (pm20) REVERT: D 614 ASP cc_start: 0.5940 (m-30) cc_final: 0.5489 (m-30) REVERT: D 684 CYS cc_start: 0.7507 (m) cc_final: 0.6997 (m) REVERT: A 148 MET cc_start: 0.6526 (mmp) cc_final: 0.6099 (mmp) REVERT: A 240 ASP cc_start: 0.7595 (OUTLIER) cc_final: 0.7218 (t0) REVERT: A 321 TRP cc_start: 0.7980 (m100) cc_final: 0.7444 (m100) REVERT: A 335 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7772 (m-80) REVERT: A 353 ASP cc_start: 0.7872 (OUTLIER) cc_final: 0.7475 (t70) REVERT: A 605 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7463 (pm20) outliers start: 134 outliers final: 63 residues processed: 252 average time/residue: 0.1199 time to fit residues: 51.3579 Evaluate side-chains 182 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 105 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 SER Chi-restraints excluded: chain B residue 125 SER Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 419 SER Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 670 LEU Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 191 GLU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 335 PHE Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 340 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 399 CYS Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 679 LEU Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 131 VAL Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 240 ASP Chi-restraints excluded: chain D residue 245 MET Chi-restraints excluded: chain D residue 257 VAL Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 363 VAL Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 605 GLU Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 767 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 240 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 687 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 179 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 258 optimal weight: 9.9990 chunk 260 optimal weight: 0.0050 chunk 73 optimal weight: 6.9990 chunk 6 optimal weight: 9.9990 chunk 235 optimal weight: 10.0000 chunk 86 optimal weight: 0.0040 chunk 67 optimal weight: 7.9990 chunk 64 optimal weight: 0.5980 chunk 203 optimal weight: 4.9990 overall best weight: 2.3210 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.041526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.034962 restraints weight = 235691.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.035892 restraints weight = 120135.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.036506 restraints weight = 75814.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.036910 restraints weight = 54723.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.037169 restraints weight = 43488.046| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22508 Z= 0.123 Angle : 0.568 10.768 30460 Z= 0.287 Chirality : 0.040 0.182 3316 Planarity : 0.004 0.039 3920 Dihedral : 6.297 110.407 3082 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.44 % Allowed : 20.52 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 aren not related in a simple way. whole: -0.59 (0.16), residues: 2744 helix: 0.59 (0.12), residues: 1740 sheet: None (None), residues: 0 loop : -2.18 (0.17), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 348 TYR 0.014 0.001 TYR D 413 PHE 0.020 0.001 PHE A 591 TRP 0.019 0.002 TRP A 129 HIS 0.006 0.001 HIS C 334 Details of bonding type rmsd covalent geometry : bond 0.00260 (22508) covalent geometry : angle 0.56758 (30460) hydrogen bonds : bond 0.04218 ( 1252) hydrogen bonds : angle 3.95796 ( 3504) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 128 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7975 (mm-30) REVERT: B 183 MET cc_start: 0.8246 (mmm) cc_final: 0.7549 (tpp) REVERT: B 360 ASN cc_start: 0.5604 (OUTLIER) cc_final: 0.5269 (p0) REVERT: B 480 GLU cc_start: 0.7946 (tt0) cc_final: 0.7654 (mt-10) REVERT: B 545 PHE cc_start: 0.5864 (OUTLIER) cc_final: 0.5629 (p90) REVERT: C 183 MET cc_start: 0.8122 (mmm) cc_final: 0.7528 (tmm) REVERT: C 194 MET cc_start: 0.7064 (mmm) cc_final: 0.6772 (mmm) REVERT: C 256 MET cc_start: 0.7040 (mmm) cc_final: 0.6347 (tmm) REVERT: C 468 MET cc_start: 0.7630 (ttm) cc_final: 0.7328 (tpp) REVERT: C 480 GLU cc_start: 0.7998 (tt0) cc_final: 0.7781 (mm-30) REVERT: C 545 PHE cc_start: 0.6028 (OUTLIER) cc_final: 0.5635 (p90) REVERT: D 114 ARG cc_start: 0.6193 (OUTLIER) cc_final: 0.5529 (mtm-85) REVERT: D 123 PHE cc_start: 0.7988 (m-80) cc_final: 0.7455 (m-80) REVERT: D 125 SER cc_start: 0.8083 (OUTLIER) cc_final: 0.7774 (m) REVERT: D 147 MET cc_start: 0.7883 (mmm) cc_final: 0.7457 (mmt) REVERT: D 153 MET cc_start: 0.8226 (ttm) cc_final: 0.7739 (mtp) REVERT: D 183 MET cc_start: 0.6067 (ppp) cc_final: 0.5716 (ppp) REVERT: D 321 TRP cc_start: 0.7801 (m100) cc_final: 0.7496 (m100) REVERT: D 476 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.7998 (mt) REVERT: D 614 ASP cc_start: 0.5941 (m-30) cc_final: 0.5620 (m-30) REVERT: D 684 CYS cc_start: 0.7430 (m) cc_final: 0.6959 (m) REVERT: A 194 MET cc_start: 0.6714 (tpp) cc_final: 0.5781 (ttt) REVERT: A 256 MET cc_start: 0.7194 (mmm) cc_final: 0.6535 (tmm) REVERT: A 321 TRP cc_start: 0.8035 (m100) cc_final: 0.7508 (m100) REVERT: A 353 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7559 (t70) REVERT: A 632 TRP cc_start: 0.7748 (OUTLIER) cc_final: 0.6799 (t60) outliers start: 106 outliers final: 54 residues processed: 227 average time/residue: 0.1334 time to fit residues: 50.1198 Evaluate side-chains 165 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 102 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 158 CYS Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 632 TRP Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 545 PHE Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 114 ARG Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 767 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 713 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 207 optimal weight: 10.0000 chunk 224 optimal weight: 7.9990 chunk 208 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 198 optimal weight: 10.0000 chunk 205 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 254 optimal weight: 20.0000 chunk 231 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 401 HIS A 334 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.040393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.033865 restraints weight = 238032.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.034769 restraints weight = 121441.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.035365 restraints weight = 77357.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.035755 restraints weight = 56410.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.036001 restraints weight = 45220.949| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 22508 Z= 0.205 Angle : 0.706 11.789 30460 Z= 0.355 Chirality : 0.043 0.177 3316 Planarity : 0.005 0.044 3920 Dihedral : 5.766 75.723 3041 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 5.53 % Allowed : 20.69 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 aren not related in a simple way. whole: -1.12 (0.15), residues: 2744 helix: 0.12 (0.12), residues: 1732 sheet: None (None), residues: 0 loop : -2.26 (0.17), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 348 TYR 0.019 0.002 TYR A 413 PHE 0.016 0.002 PHE D 763 TRP 0.014 0.002 TRP A 129 HIS 0.009 0.002 HIS C 334 Details of bonding type rmsd covalent geometry : bond 0.00445 (22508) covalent geometry : angle 0.70561 (30460) hydrogen bonds : bond 0.05292 ( 1252) hydrogen bonds : angle 4.42930 ( 3504) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 107 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.7804 (mmt) cc_final: 0.7433 (mmp) REVERT: B 245 MET cc_start: 0.7702 (tpp) cc_final: 0.7165 (ptm) REVERT: B 256 MET cc_start: 0.6074 (tmm) cc_final: 0.5843 (tmm) REVERT: B 360 ASN cc_start: 0.5866 (OUTLIER) cc_final: 0.5015 (p0) REVERT: B 480 GLU cc_start: 0.8024 (tt0) cc_final: 0.7779 (mt-10) REVERT: C 183 MET cc_start: 0.8109 (mmm) cc_final: 0.7706 (ppp) REVERT: C 256 MET cc_start: 0.6849 (mmm) cc_final: 0.6378 (tmm) REVERT: C 450 MET cc_start: 0.6513 (mmt) cc_final: 0.6018 (mmt) REVERT: C 591 PHE cc_start: 0.7814 (OUTLIER) cc_final: 0.7396 (m-80) REVERT: D 114 ARG cc_start: 0.6035 (OUTLIER) cc_final: 0.5797 (ttm110) REVERT: D 123 PHE cc_start: 0.8261 (m-80) cc_final: 0.7556 (m-80) REVERT: D 147 MET cc_start: 0.7856 (mmm) cc_final: 0.7517 (mmt) REVERT: D 148 MET cc_start: 0.5941 (OUTLIER) cc_final: 0.5488 (mmp) REVERT: D 183 MET cc_start: 0.6186 (ppp) cc_final: 0.5854 (ppp) REVERT: D 245 MET cc_start: 0.7154 (mmm) cc_final: 0.6949 (mmm) REVERT: D 321 TRP cc_start: 0.7868 (m100) cc_final: 0.7315 (m100) REVERT: D 445 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7271 (ttm170) REVERT: D 468 MET cc_start: 0.6547 (ptm) cc_final: 0.5908 (ptm) REVERT: D 476 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8229 (tp) REVERT: D 731 LEU cc_start: 0.8118 (OUTLIER) cc_final: 0.7882 (mp) REVERT: A 194 MET cc_start: 0.6659 (tpp) cc_final: 0.6010 (ttt) REVERT: A 256 MET cc_start: 0.7229 (mmm) cc_final: 0.6679 (tmm) REVERT: A 321 TRP cc_start: 0.7940 (m100) cc_final: 0.7290 (m100) REVERT: A 335 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.6623 (m-10) REVERT: A 353 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7372 (t70) REVERT: A 632 TRP cc_start: 0.7854 (OUTLIER) cc_final: 0.6694 (t60) REVERT: A 687 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8407 (pt) outliers start: 132 outliers final: 86 residues processed: 233 average time/residue: 0.1498 time to fit residues: 55.8485 Evaluate side-chains 196 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 99 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 353 ASP Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 615 ASP Chi-restraints excluded: chain C residue 626 LYS Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 114 ARG Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 445 ARG Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 731 LEU Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 335 PHE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 713 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 118 optimal weight: 6.9990 chunk 5 optimal weight: 7.9990 chunk 215 optimal weight: 20.0000 chunk 52 optimal weight: 7.9990 chunk 229 optimal weight: 10.0000 chunk 208 optimal weight: 8.9990 chunk 13 optimal weight: 9.9990 chunk 134 optimal weight: 10.0000 chunk 57 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 259 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 715 GLN C 334 HIS D 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.040480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.033861 restraints weight = 236928.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.034755 restraints weight = 121451.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.035351 restraints weight = 77694.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.035745 restraints weight = 56706.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.035995 restraints weight = 45382.627| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22508 Z= 0.224 Angle : 0.738 11.765 30460 Z= 0.374 Chirality : 0.044 0.176 3316 Planarity : 0.006 0.051 3920 Dihedral : 5.952 75.135 3038 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 15.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 6.24 % Allowed : 20.44 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 aren not related in a simple way. whole: -1.50 (0.15), residues: 2744 helix: -0.20 (0.12), residues: 1736 sheet: None (None), residues: 0 loop : -2.37 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 539 TYR 0.020 0.002 TYR A 511 PHE 0.017 0.002 PHE D 763 TRP 0.018 0.002 TRP A 129 HIS 0.009 0.002 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00485 (22508) covalent geometry : angle 0.73831 (30460) hydrogen bonds : bond 0.05610 ( 1252) hydrogen bonds : angle 4.62464 ( 3504) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 100 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.7695 (mmt) cc_final: 0.7298 (mmt) REVERT: B 256 MET cc_start: 0.6138 (tmm) cc_final: 0.5936 (tmm) REVERT: B 480 GLU cc_start: 0.8082 (tt0) cc_final: 0.7819 (mt-10) REVERT: B 591 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.7385 (m-80) REVERT: C 183 MET cc_start: 0.8108 (mmm) cc_final: 0.7583 (tmm) REVERT: C 194 MET cc_start: 0.6406 (mmm) cc_final: 0.6163 (mmm) REVERT: C 256 MET cc_start: 0.6803 (mmm) cc_final: 0.6103 (tmm) REVERT: C 450 MET cc_start: 0.6611 (mmt) cc_final: 0.6083 (mmt) REVERT: C 591 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7339 (m-80) REVERT: D 114 ARG cc_start: 0.5925 (OUTLIER) cc_final: 0.5690 (ttm110) REVERT: D 147 MET cc_start: 0.7982 (mmm) cc_final: 0.7186 (tpp) REVERT: D 148 MET cc_start: 0.6022 (OUTLIER) cc_final: 0.5590 (mmp) REVERT: D 321 TRP cc_start: 0.7961 (m100) cc_final: 0.7375 (m100) REVERT: D 445 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7421 (ttm170) REVERT: D 468 MET cc_start: 0.6543 (ptm) cc_final: 0.6258 (ptt) REVERT: D 476 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8215 (tp) REVERT: A 147 MET cc_start: 0.7409 (mmm) cc_final: 0.7122 (tpt) REVERT: A 148 MET cc_start: 0.6021 (OUTLIER) cc_final: 0.5569 (mmp) REVERT: A 194 MET cc_start: 0.6455 (tpp) cc_final: 0.6081 (ttt) REVERT: A 256 MET cc_start: 0.7193 (mmm) cc_final: 0.6755 (tmm) REVERT: A 257 VAL cc_start: 0.6804 (OUTLIER) cc_final: 0.6007 (m) REVERT: A 292 LYS cc_start: 0.8501 (mttt) cc_final: 0.8238 (mmtm) REVERT: A 321 TRP cc_start: 0.7976 (m100) cc_final: 0.7378 (m100) REVERT: A 344 ASP cc_start: 0.8224 (m-30) cc_final: 0.7984 (m-30) REVERT: A 353 ASP cc_start: 0.7918 (OUTLIER) cc_final: 0.7343 (t70) REVERT: A 605 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.6752 (pm20) REVERT: A 632 TRP cc_start: 0.7839 (OUTLIER) cc_final: 0.6762 (t60) outliers start: 149 outliers final: 102 residues processed: 239 average time/residue: 0.1168 time to fit residues: 45.6384 Evaluate side-chains 208 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 95 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 177 LEU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 83 MET Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 188 HIS Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 453 LYS Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 615 ASP Chi-restraints excluded: chain C residue 626 LYS Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 114 ARG Chi-restraints excluded: chain D residue 148 MET Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 242 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 445 ARG Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 731 LEU Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 767 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 74 optimal weight: 10.0000 chunk 34 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 197 optimal weight: 8.9990 chunk 98 optimal weight: 5.9990 chunk 137 optimal weight: 20.0000 chunk 189 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 151 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 675 GLN D 291 GLN D 678 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.040599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.033971 restraints weight = 238312.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.034877 restraints weight = 121811.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.035473 restraints weight = 77605.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.035869 restraints weight = 56428.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.036123 restraints weight = 45135.876| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 22508 Z= 0.211 Angle : 0.718 10.896 30460 Z= 0.364 Chirality : 0.043 0.172 3316 Planarity : 0.005 0.049 3920 Dihedral : 5.798 77.134 3036 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 5.74 % Allowed : 21.65 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 aren not related in a simple way. whole: -1.54 (0.15), residues: 2744 helix: -0.20 (0.12), residues: 1736 sheet: None (None), residues: 0 loop : -2.45 (0.17), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 232 TYR 0.019 0.002 TYR A 413 PHE 0.015 0.002 PHE D 763 TRP 0.018 0.002 TRP A 129 HIS 0.007 0.002 HIS B 661 Details of bonding type rmsd covalent geometry : bond 0.00457 (22508) covalent geometry : angle 0.71845 (30460) hydrogen bonds : bond 0.05518 ( 1252) hydrogen bonds : angle 4.59239 ( 3504) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 100 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.7661 (mmt) cc_final: 0.7317 (mmt) REVERT: B 245 MET cc_start: 0.7705 (tpp) cc_final: 0.7112 (ptm) REVERT: B 256 MET cc_start: 0.6058 (tmm) cc_final: 0.5858 (tmm) REVERT: B 268 ARG cc_start: 0.6215 (OUTLIER) cc_final: 0.5601 (ptm-80) REVERT: B 480 GLU cc_start: 0.8146 (tt0) cc_final: 0.7865 (mt-10) REVERT: B 591 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.7402 (m-80) REVERT: C 183 MET cc_start: 0.8184 (mmm) cc_final: 0.7560 (tmm) REVERT: C 256 MET cc_start: 0.6685 (mmm) cc_final: 0.6111 (tmm) REVERT: C 591 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7307 (m-80) REVERT: D 114 ARG cc_start: 0.5988 (OUTLIER) cc_final: 0.5748 (ttm-80) REVERT: D 147 MET cc_start: 0.7968 (mmm) cc_final: 0.7191 (tpp) REVERT: D 321 TRP cc_start: 0.7960 (m100) cc_final: 0.7415 (m100) REVERT: D 353 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7131 (p0) REVERT: D 476 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8231 (tp) REVERT: D 632 TRP cc_start: 0.7666 (OUTLIER) cc_final: 0.6563 (t60) REVERT: D 675 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7680 (mm-40) REVERT: D 731 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7845 (mp) REVERT: A 148 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.5636 (mmp) REVERT: A 194 MET cc_start: 0.6362 (tpp) cc_final: 0.6068 (ttm) REVERT: A 256 MET cc_start: 0.7111 (mmm) cc_final: 0.6695 (tmm) REVERT: A 257 VAL cc_start: 0.6825 (OUTLIER) cc_final: 0.6079 (m) REVERT: A 292 LYS cc_start: 0.8499 (mttt) cc_final: 0.8239 (mmtm) REVERT: A 321 TRP cc_start: 0.7875 (m100) cc_final: 0.7376 (m100) REVERT: A 344 ASP cc_start: 0.8190 (m-30) cc_final: 0.7938 (m-30) REVERT: A 353 ASP cc_start: 0.7923 (OUTLIER) cc_final: 0.7335 (t70) REVERT: A 605 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.6843 (pm20) outliers start: 137 outliers final: 102 residues processed: 230 average time/residue: 0.1063 time to fit residues: 40.5885 Evaluate side-chains 207 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 92 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain B residue 83 MET Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 236 LYS Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 340 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 476 LEU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 607 LEU Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 651 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 739 VAL Chi-restraints excluded: chain B residue 750 SER Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 188 HIS Chi-restraints excluded: chain C residue 213 ASP Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 615 ASP Chi-restraints excluded: chain C residue 626 LYS Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 83 MET Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 114 ARG Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 226 ILE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 304 PHE Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 512 LEU Chi-restraints excluded: chain D residue 540 SER Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 675 GLN Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 731 LEU Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 148 MET Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 293 CYS Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 363 VAL Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 731 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 139 optimal weight: 0.0870 chunk 191 optimal weight: 2.9990 chunk 197 optimal weight: 8.9990 chunk 172 optimal weight: 20.0000 chunk 265 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 154 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 48 optimal weight: 0.0770 chunk 2 optimal weight: 0.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 675 GLN D 243 HIS A 401 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.042076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.035554 restraints weight = 231908.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.036479 restraints weight = 117552.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.037089 restraints weight = 74029.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.037488 restraints weight = 53407.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.037752 restraints weight = 42482.300| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22508 Z= 0.109 Angle : 0.559 10.316 30460 Z= 0.280 Chirality : 0.039 0.178 3316 Planarity : 0.003 0.039 3920 Dihedral : 4.919 76.348 3035 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 2.81 % Allowed : 24.37 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 aren not related in a simple way. whole: -0.51 (0.16), residues: 2744 helix: 0.65 (0.13), residues: 1748 sheet: None (None), residues: 0 loop : -2.16 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 232 TYR 0.010 0.001 TYR B 413 PHE 0.012 0.001 PHE D 522 TRP 0.017 0.001 TRP A 129 HIS 0.003 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00227 (22508) covalent geometry : angle 0.55903 (30460) hydrogen bonds : bond 0.03965 ( 1252) hydrogen bonds : angle 3.87389 ( 3504) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 126 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.8027 (mm-30) REVERT: B 194 MET cc_start: 0.7718 (mmt) cc_final: 0.7380 (mmp) REVERT: B 240 ASP cc_start: 0.8717 (p0) cc_final: 0.8430 (m-30) REVERT: B 245 MET cc_start: 0.7551 (tpp) cc_final: 0.6982 (ptm) REVERT: B 256 MET cc_start: 0.6376 (tmm) cc_final: 0.6107 (tmm) REVERT: B 714 MET cc_start: 0.8148 (tpp) cc_final: 0.7871 (tpp) REVERT: C 183 MET cc_start: 0.8348 (mmm) cc_final: 0.7763 (tmm) REVERT: D 147 MET cc_start: 0.7911 (mmm) cc_final: 0.7594 (mmm) REVERT: D 183 MET cc_start: 0.6044 (mtm) cc_final: 0.5517 (mmm) REVERT: D 321 TRP cc_start: 0.7895 (m100) cc_final: 0.7234 (m100) REVERT: D 429 VAL cc_start: 0.7768 (OUTLIER) cc_final: 0.7531 (t) REVERT: D 632 TRP cc_start: 0.7773 (OUTLIER) cc_final: 0.6717 (t60) REVERT: A 147 MET cc_start: 0.7421 (tmm) cc_final: 0.7078 (tpt) REVERT: A 194 MET cc_start: 0.6227 (tpp) cc_final: 0.5765 (ttt) REVERT: A 256 MET cc_start: 0.7238 (mmm) cc_final: 0.6741 (tmm) REVERT: A 257 VAL cc_start: 0.6863 (OUTLIER) cc_final: 0.6106 (m) REVERT: A 292 LYS cc_start: 0.8497 (mttt) cc_final: 0.8245 (mmtm) REVERT: A 321 TRP cc_start: 0.7798 (m100) cc_final: 0.7304 (m100) REVERT: A 353 ASP cc_start: 0.7956 (OUTLIER) cc_final: 0.7295 (t70) REVERT: A 605 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7183 (pm20) REVERT: A 632 TRP cc_start: 0.8032 (OUTLIER) cc_final: 0.6988 (t60) outliers start: 67 outliers final: 33 residues processed: 190 average time/residue: 0.1098 time to fit residues: 35.3631 Evaluate side-chains 147 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 107 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 663 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 259 optimal weight: 7.9990 chunk 93 optimal weight: 0.3980 chunk 155 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 107 optimal weight: 10.0000 chunk 229 optimal weight: 9.9990 chunk 123 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 222 optimal weight: 5.9990 chunk 166 optimal weight: 0.0370 chunk 143 optimal weight: 20.0000 overall best weight: 2.4864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 675 GLN C 442 GLN A 188 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.041499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.034939 restraints weight = 233631.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.035867 restraints weight = 118750.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.036471 restraints weight = 74816.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.036870 restraints weight = 54005.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.037127 restraints weight = 43003.682| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.4991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22508 Z= 0.123 Angle : 0.591 10.639 30460 Z= 0.293 Chirality : 0.040 0.178 3316 Planarity : 0.004 0.037 3920 Dihedral : 4.733 77.959 3027 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.93 % Allowed : 24.46 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 aren not related in a simple way. whole: -0.51 (0.16), residues: 2744 helix: 0.65 (0.12), residues: 1756 sheet: None (None), residues: 0 loop : -2.19 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 232 TYR 0.017 0.001 TYR B 466 PHE 0.012 0.001 PHE D 198 TRP 0.015 0.001 TRP A 129 HIS 0.003 0.001 HIS A 357 Details of bonding type rmsd covalent geometry : bond 0.00269 (22508) covalent geometry : angle 0.59066 (30460) hydrogen bonds : bond 0.04283 ( 1252) hydrogen bonds : angle 3.93986 ( 3504) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 112 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 147 MET cc_start: 0.6558 (tpp) cc_final: 0.6250 (tmm) REVERT: B 173 GLU cc_start: 0.8289 (OUTLIER) cc_final: 0.8002 (mm-30) REVERT: B 194 MET cc_start: 0.7693 (mmt) cc_final: 0.7366 (mmp) REVERT: B 240 ASP cc_start: 0.8717 (p0) cc_final: 0.8428 (m-30) REVERT: B 256 MET cc_start: 0.6312 (tmm) cc_final: 0.6023 (tmm) REVERT: B 591 PHE cc_start: 0.7955 (OUTLIER) cc_final: 0.7705 (m-80) REVERT: B 661 HIS cc_start: 0.6885 (m-70) cc_final: 0.6518 (m170) REVERT: C 183 MET cc_start: 0.8331 (mmm) cc_final: 0.7834 (tmm) REVERT: C 256 MET cc_start: 0.6676 (mmm) cc_final: 0.6436 (mtt) REVERT: D 147 MET cc_start: 0.7902 (mmm) cc_final: 0.7524 (mmm) REVERT: D 321 TRP cc_start: 0.7749 (m100) cc_final: 0.7180 (m100) REVERT: D 468 MET cc_start: 0.7373 (tmm) cc_final: 0.7088 (tmm) REVERT: D 476 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8206 (tp) REVERT: D 632 TRP cc_start: 0.7719 (OUTLIER) cc_final: 0.6732 (t60) REVERT: D 737 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8609 (tt) REVERT: A 147 MET cc_start: 0.7279 (mmm) cc_final: 0.6959 (tpt) REVERT: A 194 MET cc_start: 0.6381 (tpp) cc_final: 0.5962 (ttt) REVERT: A 256 MET cc_start: 0.7201 (mmm) cc_final: 0.6694 (tmm) REVERT: A 257 VAL cc_start: 0.6879 (OUTLIER) cc_final: 0.6139 (m) REVERT: A 292 LYS cc_start: 0.8542 (mttt) cc_final: 0.8282 (mmtm) REVERT: A 321 TRP cc_start: 0.7788 (m100) cc_final: 0.7263 (m100) REVERT: A 353 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7269 (t70) REVERT: A 632 TRP cc_start: 0.7938 (OUTLIER) cc_final: 0.6796 (t60) outliers start: 70 outliers final: 52 residues processed: 181 average time/residue: 0.1058 time to fit residues: 33.0597 Evaluate side-chains 163 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 103 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 615 ASP Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 767 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 45 optimal weight: 6.9990 chunk 241 optimal weight: 10.0000 chunk 150 optimal weight: 4.9990 chunk 193 optimal weight: 7.9990 chunk 271 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 254 optimal weight: 8.9990 chunk 154 optimal weight: 8.9990 chunk 65 optimal weight: 0.9980 chunk 105 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.040928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.034309 restraints weight = 238086.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.035232 restraints weight = 121371.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.035835 restraints weight = 76864.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.036234 restraints weight = 55499.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.036499 restraints weight = 44264.564| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 22508 Z= 0.189 Angle : 0.693 10.146 30460 Z= 0.347 Chirality : 0.043 0.191 3316 Planarity : 0.005 0.045 3920 Dihedral : 5.190 80.468 3027 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 3.27 % Allowed : 24.37 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 aren not related in a simple way. whole: -1.04 (0.15), residues: 2744 helix: 0.23 (0.12), residues: 1748 sheet: None (None), residues: 0 loop : -2.34 (0.17), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 232 TYR 0.017 0.002 TYR A 413 PHE 0.013 0.002 PHE B 545 TRP 0.016 0.002 TRP A 129 HIS 0.007 0.002 HIS C 334 Details of bonding type rmsd covalent geometry : bond 0.00413 (22508) covalent geometry : angle 0.69350 (30460) hydrogen bonds : bond 0.05139 ( 1252) hydrogen bonds : angle 4.34401 ( 3504) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 106 time to evaluate : 0.854 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8454 (tt) REVERT: B 173 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7951 (mm-30) REVERT: B 194 MET cc_start: 0.7654 (mmt) cc_final: 0.7303 (mmt) REVERT: B 245 MET cc_start: 0.7336 (tpp) cc_final: 0.6833 (ptm) REVERT: B 256 MET cc_start: 0.6158 (tmm) cc_final: 0.5933 (tmm) REVERT: B 591 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7749 (m-80) REVERT: C 189 GLU cc_start: 0.3113 (mt-10) cc_final: 0.2876 (mm-30) REVERT: C 450 MET cc_start: 0.6337 (mpp) cc_final: 0.5023 (mmt) REVERT: D 147 MET cc_start: 0.7909 (mmm) cc_final: 0.7603 (mmm) REVERT: D 321 TRP cc_start: 0.7791 (m100) cc_final: 0.7292 (m100) REVERT: D 468 MET cc_start: 0.7314 (tmm) cc_final: 0.7095 (tmm) REVERT: D 476 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8258 (tp) REVERT: D 632 TRP cc_start: 0.7698 (OUTLIER) cc_final: 0.6645 (t60) REVERT: D 737 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8678 (tt) REVERT: A 194 MET cc_start: 0.6337 (tpp) cc_final: 0.5905 (ttt) REVERT: A 256 MET cc_start: 0.7125 (mmm) cc_final: 0.6670 (tmm) REVERT: A 257 VAL cc_start: 0.6926 (OUTLIER) cc_final: 0.6190 (m) REVERT: A 292 LYS cc_start: 0.8529 (mttt) cc_final: 0.8278 (mmtm) REVERT: A 321 TRP cc_start: 0.7857 (m100) cc_final: 0.7379 (m100) REVERT: A 353 ASP cc_start: 0.7889 (OUTLIER) cc_final: 0.7174 (t70) REVERT: A 632 TRP cc_start: 0.7863 (OUTLIER) cc_final: 0.6849 (t60) REVERT: A 731 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7603 (mp) outliers start: 78 outliers final: 59 residues processed: 183 average time/residue: 0.1405 time to fit residues: 43.3660 Evaluate side-chains 168 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 99 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 591 PHE Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 615 ASP Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 111 LEU Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 621 LEU Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain A residue 713 GLU Chi-restraints excluded: chain A residue 731 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 217 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 75 optimal weight: 7.9990 chunk 166 optimal weight: 4.9990 chunk 253 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.041875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.035299 restraints weight = 232230.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.036224 restraints weight = 118027.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.036832 restraints weight = 74597.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.037241 restraints weight = 53773.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.037494 restraints weight = 42725.076| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.5190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22508 Z= 0.115 Angle : 0.597 12.139 30460 Z= 0.293 Chirality : 0.040 0.185 3316 Planarity : 0.004 0.038 3920 Dihedral : 4.759 80.677 3027 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.60 % Allowed : 24.83 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 aren not related in a simple way. whole: -0.56 (0.16), residues: 2744 helix: 0.60 (0.12), residues: 1760 sheet: None (None), residues: 0 loop : -2.19 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 114 TYR 0.012 0.001 TYR B 416 PHE 0.012 0.001 PHE D 198 TRP 0.016 0.001 TRP A 129 HIS 0.003 0.001 HIS C 357 Details of bonding type rmsd covalent geometry : bond 0.00251 (22508) covalent geometry : angle 0.59657 (30460) hydrogen bonds : bond 0.04201 ( 1252) hydrogen bonds : angle 3.94661 ( 3504) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5488 Ramachandran restraints generated. 2744 Oldfield, 0 Emsley, 2744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 106 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 91 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8440 (tt) REVERT: B 147 MET cc_start: 0.6650 (tpp) cc_final: 0.6367 (tmm) REVERT: B 173 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8025 (mm-30) REVERT: B 194 MET cc_start: 0.7641 (mmt) cc_final: 0.7279 (mmp) REVERT: B 245 MET cc_start: 0.7303 (tpp) cc_final: 0.6779 (ptm) REVERT: B 256 MET cc_start: 0.6340 (tmm) cc_final: 0.6063 (tmm) REVERT: C 189 GLU cc_start: 0.3102 (mt-10) cc_final: 0.2873 (mm-30) REVERT: C 256 MET cc_start: 0.6909 (mtt) cc_final: 0.6229 (mmm) REVERT: D 147 MET cc_start: 0.7934 (mmm) cc_final: 0.7505 (mmm) REVERT: D 321 TRP cc_start: 0.7746 (m100) cc_final: 0.7260 (m100) REVERT: D 468 MET cc_start: 0.7414 (tmm) cc_final: 0.7145 (tmm) REVERT: D 476 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8165 (tp) REVERT: D 632 TRP cc_start: 0.7717 (OUTLIER) cc_final: 0.6562 (t60) REVERT: D 737 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8637 (tt) REVERT: A 148 MET cc_start: 0.6220 (mmp) cc_final: 0.5943 (mmp) REVERT: A 194 MET cc_start: 0.6329 (tpp) cc_final: 0.5888 (ttt) REVERT: A 256 MET cc_start: 0.7283 (mmm) cc_final: 0.6773 (tmm) REVERT: A 257 VAL cc_start: 0.6975 (OUTLIER) cc_final: 0.6251 (m) REVERT: A 292 LYS cc_start: 0.8496 (mttt) cc_final: 0.8253 (mmtm) REVERT: A 321 TRP cc_start: 0.7741 (m100) cc_final: 0.7250 (m100) REVERT: A 353 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7167 (t70) REVERT: A 468 MET cc_start: 0.7445 (tpp) cc_final: 0.7139 (ptt) REVERT: A 632 TRP cc_start: 0.7955 (OUTLIER) cc_final: 0.6956 (t60) REVERT: A 713 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7753 (pm20) outliers start: 62 outliers final: 46 residues processed: 167 average time/residue: 0.1234 time to fit residues: 35.2246 Evaluate side-chains 153 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 98 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LEU Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 337 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 615 ASP Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 177 LEU Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 476 LEU Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 608 ILE Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 737 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 353 ASP Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 632 TRP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 713 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 13 optimal weight: 20.0000 chunk 131 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 208 optimal weight: 8.9990 chunk 248 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 183 optimal weight: 7.9990 chunk 231 optimal weight: 0.0070 overall best weight: 3.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.041344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.034708 restraints weight = 235588.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.035643 restraints weight = 120309.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.036253 restraints weight = 76193.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.036604 restraints weight = 55047.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.036888 restraints weight = 45043.012| |-----------------------------------------------------------------------------| r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.5264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22508 Z= 0.153 Angle : 0.653 12.439 30460 Z= 0.323 Chirality : 0.041 0.181 3316 Planarity : 0.004 0.043 3920 Dihedral : 4.940 81.272 3027 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.10 % Allowed : 24.37 % Favored : 72.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % 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 aren not related in a simple way. whole: -0.70 (0.16), residues: 2744 helix: 0.49 (0.12), residues: 1740 sheet: None (None), residues: 0 loop : -2.20 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 232 TYR 0.016 0.002 TYR A 413 PHE 0.014 0.001 PHE B 545 TRP 0.015 0.002 TRP A 129 HIS 0.005 0.001 HIS C 334 Details of bonding type rmsd covalent geometry : bond 0.00337 (22508) covalent geometry : angle 0.65304 (30460) hydrogen bonds : bond 0.04691 ( 1252) hydrogen bonds : angle 4.15073 ( 3504) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3322.26 seconds wall clock time: 58 minutes 30.10 seconds (3510.10 seconds total)