Starting phenix.real_space_refine on Wed May 21 23:08:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i6p_35202/05_2025/8i6p_35202.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i6p_35202/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8i6p_35202/05_2025/8i6p_35202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i6p_35202/05_2025/8i6p_35202.map" model { file = "/net/cci-nas-00/data/ceres_data/8i6p_35202/05_2025/8i6p_35202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i6p_35202/05_2025/8i6p_35202.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 11.79, per 1000 atoms: 0.54 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: 5.83 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 2.35 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: 7.15 Time building geometry restraints manager: 6.77 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.190 Set scattering table: 0.210 Process input model: 48.080 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.050 ------------------------------------------------------------------------------- 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 : 21.69 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (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 TRP 0.011 0.002 TRP C 321 HIS 0.004 0.001 HIS D 334 PHE 0.009 0.001 PHE D 294 TYR 0.012 0.001 TYR A 466 ARG 0.005 0.001 ARG D 593 Details of bonding type rmsd hydrogen bonds : bond 0.13418 ( 1252) hydrogen bonds : angle 5.81048 ( 3504) covalent geometry : bond 0.00547 (22508) covalent geometry : angle 0.76003 (30460) *********************** 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 : 2.859 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: 0.3104 time to fit residues: 266.3298 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 : 2.751 ------------------------------------------------------------------------------- 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 229 optimal weight: 4.9990 chunk 206 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 213 optimal weight: 4.9990 chunk 82 optimal weight: 0.9980 chunk 129 optimal weight: 9.9990 chunk 158 optimal weight: 5.9990 chunk 247 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- 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 678 GLN B 709 GLN B 764 GLN C 531 ASN C 678 GLN C 709 GLN C 764 GLN D 334 HIS D 357 HIS D 531 ASN D 551 GLN D 709 GLN D 757 HIS D 764 GLN A 291 GLN A 334 HIS A 357 HIS A 405 ASN A 531 ASN A 551 GLN A 590 HIS A 709 GLN A 757 HIS ** A 764 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.040737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.034090 restraints weight = 236705.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.034995 restraints weight = 122871.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.035571 restraints weight = 78785.765| |-----------------------------------------------------------------------------| r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 22508 Z= 0.167 Angle : 0.649 10.260 30460 Z= 0.334 Chirality : 0.043 0.172 3316 Planarity : 0.005 0.055 3920 Dihedral : 9.547 150.914 3246 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 6.16 % Allowed : 21.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.15), residues: 2744 helix: -0.28 (0.12), residues: 1728 sheet: None (None), residues: 0 loop : -2.44 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 129 HIS 0.010 0.002 HIS B 334 PHE 0.015 0.002 PHE B 566 TYR 0.017 0.002 TYR A 413 ARG 0.012 0.001 ARG C 348 Details of bonding type rmsd hydrogen bonds : bond 0.05105 ( 1252) hydrogen bonds : angle 4.45403 ( 3504) covalent geometry : bond 0.00360 (22508) covalent geometry : angle 0.64865 (30460) *********************** 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 268 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 121 time to evaluate : 2.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 MET cc_start: 0.8398 (mmm) cc_final: 0.7704 (tpp) REVERT: B 194 MET cc_start: 0.7924 (mmt) cc_final: 0.7508 (tpp) REVERT: B 476 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8023 (mp) REVERT: B 480 GLU cc_start: 0.8088 (tt0) cc_final: 0.7805 (mt-10) REVERT: B 541 ASN cc_start: 0.7346 (t0) cc_final: 0.7091 (t0) REVERT: B 549 ASP cc_start: 0.5760 (OUTLIER) cc_final: 0.5108 (p0) REVERT: B 607 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8213 (tp) REVERT: B 734 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: C 183 MET cc_start: 0.8276 (mmm) cc_final: 0.7821 (ppp) REVERT: C 240 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8299 (p0) REVERT: C 256 MET cc_start: 0.7147 (mmm) cc_final: 0.6549 (tmm) REVERT: C 398 PHE cc_start: 0.5987 (m-80) cc_final: 0.5569 (m-80) REVERT: C 400 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7443 (tt) REVERT: C 450 MET cc_start: 0.6150 (mmt) cc_final: 0.5509 (mmt) REVERT: C 476 LEU cc_start: 0.8252 (OUTLIER) cc_final: 0.7768 (mt) REVERT: C 480 GLU cc_start: 0.8119 (tt0) cc_final: 0.7662 (mt-10) REVERT: C 609 SER cc_start: 0.8245 (OUTLIER) cc_final: 0.8038 (m) REVERT: D 123 PHE cc_start: 0.7920 (m-80) cc_final: 0.7313 (m-80) REVERT: D 125 SER cc_start: 0.8029 (OUTLIER) cc_final: 0.7747 (m) REVERT: D 245 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7377 (mmm) REVERT: D 321 TRP cc_start: 0.7868 (m100) cc_final: 0.7431 (m100) REVERT: D 614 ASP cc_start: 0.6229 (m-30) cc_final: 0.5841 (m-30) REVERT: D 684 CYS cc_start: 0.7498 (m) cc_final: 0.6930 (m) REVERT: A 240 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7213 (t0) REVERT: A 321 TRP cc_start: 0.8021 (m100) cc_final: 0.7459 (m100) REVERT: A 335 PHE cc_start: 0.8086 (OUTLIER) cc_final: 0.7781 (m-80) REVERT: A 353 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7480 (t70) REVERT: A 632 TRP cc_start: 0.7637 (OUTLIER) cc_final: 0.7259 (t60) outliers start: 147 outliers final: 78 residues processed: 258 average time/residue: 0.2791 time to fit residues: 120.0542 Evaluate side-chains 196 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 104 time to evaluate : 2.671 ------------------------------------------------------------------------------- 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 351 THR Chi-restraints excluded: chain B residue 353 ASP 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 476 LEU Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 549 ASP 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 651 VAL Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 679 LEU Chi-restraints excluded: chain B residue 680 THR Chi-restraints excluded: chain B residue 703 VAL Chi-restraints excluded: chain B residue 734 GLU 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 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 337 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 399 CYS Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 414 ASN 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 609 SER Chi-restraints excluded: chain C residue 664 THR Chi-restraints excluded: chain C residue 680 THR Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 85 ASP 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 226 ILE Chi-restraints excluded: chain D residue 245 MET 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 363 VAL Chi-restraints excluded: chain D residue 366 ILE 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 554 LEU Chi-restraints excluded: chain D residue 587 VAL Chi-restraints excluded: chain D residue 601 THR Chi-restraints excluded: chain D residue 618 SER Chi-restraints excluded: chain D residue 664 THR Chi-restraints excluded: chain D residue 688 SER Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 767 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 226 ILE 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 409 VAL Chi-restraints excluded: chain A residue 429 VAL 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 632 TRP Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 685 CYS 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 186 optimal weight: 20.0000 chunk 147 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 231 optimal weight: 5.9990 chunk 259 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 chunk 213 optimal weight: 9.9990 chunk 236 optimal weight: 0.8980 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 166 ASN A 764 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.041158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.034625 restraints weight = 234577.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.035542 restraints weight = 119874.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.036142 restraints weight = 75785.233| |-----------------------------------------------------------------------------| r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22508 Z= 0.137 Angle : 0.590 9.993 30460 Z= 0.301 Chirality : 0.040 0.176 3316 Planarity : 0.004 0.042 3920 Dihedral : 6.529 86.906 3087 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.90 % Allowed : 21.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.15), residues: 2744 helix: 0.38 (0.12), residues: 1728 sheet: None (None), residues: 0 loop : -2.27 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 129 HIS 0.006 0.001 HIS C 334 PHE 0.014 0.001 PHE D 198 TYR 0.013 0.001 TYR D 413 ARG 0.005 0.001 ARG C 348 Details of bonding type rmsd hydrogen bonds : bond 0.04512 ( 1252) hydrogen bonds : angle 4.12946 ( 3504) covalent geometry : bond 0.00293 (22508) covalent geometry : angle 0.59008 (30460) *********************** 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 233 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 116 time to evaluate : 2.468 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 148 MET cc_start: 0.6844 (mmp) cc_final: 0.6618 (mmm) REVERT: B 183 MET cc_start: 0.8279 (mmm) cc_final: 0.7615 (tpp) REVERT: B 360 ASN cc_start: 0.5567 (OUTLIER) cc_final: 0.5247 (p0) REVERT: B 480 GLU cc_start: 0.7989 (tt0) cc_final: 0.7703 (mt-10) REVERT: C 183 MET cc_start: 0.8160 (mmm) cc_final: 0.7561 (tmm) REVERT: C 400 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7448 (tt) REVERT: C 414 ASN cc_start: 0.8455 (OUTLIER) cc_final: 0.7787 (p0) REVERT: C 480 GLU cc_start: 0.8096 (tt0) cc_final: 0.7655 (mt-10) REVERT: C 538 LEU cc_start: 0.8364 (tp) cc_final: 0.8156 (pp) REVERT: C 545 PHE cc_start: 0.6162 (OUTLIER) cc_final: 0.5841 (p90) REVERT: D 114 ARG cc_start: 0.6114 (OUTLIER) cc_final: 0.5809 (ttm110) REVERT: D 123 PHE cc_start: 0.8182 (m-80) cc_final: 0.7566 (m-80) REVERT: D 183 MET cc_start: 0.6947 (mmm) cc_final: 0.6547 (ppp) REVERT: D 245 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7437 (mmm) REVERT: D 321 TRP cc_start: 0.7757 (m100) cc_final: 0.7384 (m100) REVERT: D 684 CYS cc_start: 0.7473 (m) cc_final: 0.6914 (m) REVERT: A 321 TRP cc_start: 0.7941 (m100) cc_final: 0.7370 (m100) REVERT: A 353 ASP cc_start: 0.7943 (OUTLIER) cc_final: 0.7483 (t70) outliers start: 117 outliers final: 71 residues processed: 226 average time/residue: 0.2773 time to fit residues: 104.6529 Evaluate side-chains 180 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 102 time to evaluate : 2.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 ASN 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 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 542 LEU 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 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 83 MET Chi-restraints excluded: chain C residue 125 SER Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 248 THR 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 400 LEU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 414 ASN 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 685 CYS Chi-restraints excluded: chain C residue 687 LEU 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 158 CYS Chi-restraints excluded: chain D residue 213 ASP Chi-restraints excluded: chain D residue 245 MET 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 363 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 554 LEU Chi-restraints excluded: chain D residue 601 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 91 LEU 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 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 429 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 683 ILE Chi-restraints excluded: chain A residue 685 CYS Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 767 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 235 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 17 optimal weight: 7.9990 chunk 226 optimal weight: 7.9990 chunk 96 optimal weight: 20.0000 chunk 181 optimal weight: 6.9990 chunk 248 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 254 optimal weight: 6.9990 chunk 227 optimal weight: 4.9990 chunk 206 optimal weight: 7.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.040694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.034089 restraints weight = 239887.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.034996 restraints weight = 122090.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.035610 restraints weight = 77097.497| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 22508 Z= 0.182 Angle : 0.673 11.468 30460 Z= 0.340 Chirality : 0.042 0.164 3316 Planarity : 0.005 0.045 3920 Dihedral : 6.277 74.374 3060 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 6.16 % Allowed : 20.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.15), residues: 2744 helix: 0.13 (0.12), residues: 1740 sheet: None (None), residues: 0 loop : -2.35 (0.17), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 129 HIS 0.008 0.002 HIS A 357 PHE 0.014 0.002 PHE D 198 TYR 0.018 0.002 TYR A 413 ARG 0.007 0.001 ARG B 574 Details of bonding type rmsd hydrogen bonds : bond 0.05196 ( 1252) hydrogen bonds : angle 4.39269 ( 3504) covalent geometry : bond 0.00396 (22508) covalent geometry : angle 0.67325 (30460) *********************** 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 250 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 103 time to evaluate : 2.519 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 173 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8048 (mm-30) REVERT: B 183 MET cc_start: 0.8448 (mmm) cc_final: 0.7870 (tpp) REVERT: B 194 MET cc_start: 0.7791 (mmt) cc_final: 0.7416 (mmt) REVERT: B 245 MET cc_start: 0.7790 (tpp) cc_final: 0.7298 (ptm) REVERT: B 480 GLU cc_start: 0.8072 (tt0) cc_final: 0.7803 (mt-10) REVERT: B 591 PHE cc_start: 0.7850 (OUTLIER) cc_final: 0.7513 (m-80) REVERT: C 183 MET cc_start: 0.8117 (mmm) cc_final: 0.7473 (tmm) REVERT: C 194 MET cc_start: 0.7793 (mmt) cc_final: 0.7371 (mmp) REVERT: C 400 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7460 (tp) REVERT: C 476 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7910 (mt) REVERT: C 480 GLU cc_start: 0.8129 (tt0) cc_final: 0.7859 (mt-10) REVERT: C 591 PHE cc_start: 0.7854 (OUTLIER) cc_final: 0.7515 (m-80) REVERT: D 114 ARG cc_start: 0.6072 (OUTLIER) cc_final: 0.5847 (ttm110) REVERT: D 123 PHE cc_start: 0.8165 (m-80) cc_final: 0.7660 (m-80) REVERT: D 148 MET cc_start: 0.6211 (OUTLIER) cc_final: 0.5695 (mmp) REVERT: D 321 TRP cc_start: 0.7799 (m100) cc_final: 0.7190 (m100) REVERT: D 731 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7904 (mp) REVERT: A 321 TRP cc_start: 0.7915 (m100) cc_final: 0.7263 (m100) REVERT: A 335 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.6372 (m-10) REVERT: A 353 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7459 (t70) REVERT: A 605 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.6720 (pm20) outliers start: 147 outliers final: 93 residues processed: 243 average time/residue: 0.2962 time to fit residues: 115.8980 Evaluate side-chains 197 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 93 time to evaluate : 2.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 THR 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 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 494 VAL Chi-restraints excluded: chain B residue 542 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 615 ASP Chi-restraints excluded: chain B residue 662 VAL 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 83 MET 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 248 THR 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 383 VAL Chi-restraints excluded: chain C residue 399 CYS Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 414 ASN Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 542 LEU 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 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 242 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 363 VAL 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 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 91 LEU 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 173 GLU Chi-restraints excluded: chain A residue 213 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 196 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 213 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 29 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 160 optimal weight: 6.9990 chunk 265 optimal weight: 0.8980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 401 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.041380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.034826 restraints weight = 234656.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.035742 restraints weight = 119019.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.036347 restraints weight = 75194.001| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22508 Z= 0.123 Angle : 0.573 10.506 30460 Z= 0.288 Chirality : 0.040 0.162 3316 Planarity : 0.004 0.039 3920 Dihedral : 5.777 74.590 3054 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.73 % Allowed : 21.65 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.15), residues: 2744 helix: 0.55 (0.12), residues: 1728 sheet: None (None), residues: 0 loop : -2.25 (0.17), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 129 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE D 198 TYR 0.012 0.001 TYR A 413 ARG 0.006 0.000 ARG C 114 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 1252) hydrogen bonds : angle 4.04395 ( 3504) covalent geometry : bond 0.00263 (22508) covalent geometry : angle 0.57278 (30460) *********************** 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 217 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 104 time to evaluate : 2.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 173 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.8067 (mm-30) REVERT: B 194 MET cc_start: 0.7796 (mmt) cc_final: 0.7409 (mmt) REVERT: B 480 GLU cc_start: 0.8051 (tt0) cc_final: 0.7781 (mt-10) REVERT: C 183 MET cc_start: 0.8151 (mmm) cc_final: 0.7609 (tmm) REVERT: C 194 MET cc_start: 0.7806 (mmt) cc_final: 0.7383 (mmp) REVERT: C 400 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7474 (tt) REVERT: C 476 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7875 (mt) REVERT: C 591 PHE cc_start: 0.7902 (OUTLIER) cc_final: 0.7600 (m-80) REVERT: C 656 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8035 (tp) REVERT: D 114 ARG cc_start: 0.6135 (OUTLIER) cc_final: 0.5847 (ttm-80) REVERT: D 321 TRP cc_start: 0.7755 (m100) cc_final: 0.7245 (m100) REVERT: D 468 MET cc_start: 0.7245 (tmm) cc_final: 0.6737 (tmm) REVERT: A 257 VAL cc_start: 0.6725 (OUTLIER) cc_final: 0.5965 (m) REVERT: A 321 TRP cc_start: 0.7824 (m100) cc_final: 0.7262 (m100) REVERT: A 353 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7384 (t70) REVERT: A 605 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.6874 (pm20) REVERT: A 731 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7700 (mp) outliers start: 113 outliers final: 72 residues processed: 215 average time/residue: 0.2712 time to fit residues: 97.8485 Evaluate side-chains 180 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 98 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 494 VAL Chi-restraints excluded: chain B residue 542 LEU 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 687 LEU Chi-restraints excluded: chain B residue 703 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 146 PHE Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 383 VAL Chi-restraints excluded: chain C residue 399 CYS Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 429 VAL Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain C residue 494 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 656 ILE Chi-restraints excluded: chain C residue 662 VAL 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 114 ARG Chi-restraints excluded: chain D residue 158 CYS 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 363 VAL 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 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 683 ILE 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 158 CYS Chi-restraints excluded: chain A residue 177 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 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 687 LEU Chi-restraints excluded: chain A residue 710 VAL 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 20 optimal weight: 8.9990 chunk 270 optimal weight: 6.9990 chunk 203 optimal weight: 8.9990 chunk 262 optimal weight: 0.0030 chunk 227 optimal weight: 10.0000 chunk 36 optimal weight: 6.9990 chunk 233 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 265 optimal weight: 0.0980 chunk 169 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 overall best weight: 3.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 675 GLN C 334 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.041264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.034715 restraints weight = 234976.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.035637 restraints weight = 120300.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.036240 restraints weight = 75717.452| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.4453 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= 0.133 Angle : 0.593 10.422 30460 Z= 0.297 Chirality : 0.040 0.152 3316 Planarity : 0.004 0.052 3920 Dihedral : 5.530 75.749 3048 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.90 % Allowed : 21.48 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.16), residues: 2744 helix: 0.59 (0.12), residues: 1740 sheet: None (None), residues: 0 loop : -2.26 (0.17), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 129 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE D 198 TYR 0.013 0.001 TYR D 413 ARG 0.010 0.001 ARG D 539 Details of bonding type rmsd hydrogen bonds : bond 0.04501 ( 1252) hydrogen bonds : angle 4.05000 ( 3504) covalent geometry : bond 0.00289 (22508) covalent geometry : angle 0.59281 (30460) *********************** 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 220 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 103 time to evaluate : 3.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 91 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8544 (tt) REVERT: B 147 MET cc_start: 0.6725 (tpp) cc_final: 0.6419 (tpt) REVERT: B 173 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8024 (mm-30) REVERT: B 194 MET cc_start: 0.7757 (mmt) cc_final: 0.7387 (mmt) REVERT: B 268 ARG cc_start: 0.6127 (OUTLIER) cc_final: 0.5534 (ptm-80) REVERT: B 480 GLU cc_start: 0.8048 (tt0) cc_final: 0.7767 (mt-10) REVERT: B 591 PHE cc_start: 0.7941 (OUTLIER) cc_final: 0.7682 (m-80) REVERT: C 183 MET cc_start: 0.8141 (mmm) cc_final: 0.7539 (tmm) REVERT: C 194 MET cc_start: 0.7742 (mmt) cc_final: 0.7367 (mmp) REVERT: C 256 MET cc_start: 0.6987 (mtt) cc_final: 0.6420 (mmm) REVERT: C 414 ASN cc_start: 0.8405 (OUTLIER) cc_final: 0.7813 (p0) REVERT: C 591 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7643 (m-80) REVERT: C 656 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.8041 (tp) REVERT: D 114 ARG cc_start: 0.6074 (OUTLIER) cc_final: 0.5787 (ttm110) REVERT: D 148 MET cc_start: 0.6093 (OUTLIER) cc_final: 0.5474 (mmp) REVERT: D 321 TRP cc_start: 0.7812 (m100) cc_final: 0.7288 (m100) REVERT: A 292 LYS cc_start: 0.8517 (mttt) cc_final: 0.8255 (mmtm) REVERT: A 321 TRP cc_start: 0.7856 (m100) cc_final: 0.7316 (m100) REVERT: A 353 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7331 (t70) REVERT: A 605 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.6974 (pm20) REVERT: A 632 TRP cc_start: 0.7706 (OUTLIER) cc_final: 0.6787 (t60) REVERT: A 731 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7691 (mp) outliers start: 117 outliers final: 83 residues processed: 215 average time/residue: 0.2932 time to fit residues: 104.2394 Evaluate side-chains 191 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 95 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 91 LEU 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 268 ARG 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 409 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 542 LEU 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 703 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 240 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 383 VAL Chi-restraints excluded: chain C residue 399 CYS Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 414 ASN 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 591 PHE Chi-restraints excluded: chain C residue 615 ASP Chi-restraints excluded: chain C residue 626 LYS Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 662 VAL 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 242 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 363 VAL 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 512 LEU 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 683 ILE 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 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 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 687 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 767 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 186 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 112 optimal weight: 6.9990 chunk 177 optimal weight: 0.6980 chunk 267 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 140 optimal weight: 20.0000 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 442 GLN D 349 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.041138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.034539 restraints weight = 235500.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.035439 restraints weight = 120028.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.036022 restraints weight = 76051.476| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22508 Z= 0.155 Angle : 0.633 10.825 30460 Z= 0.316 Chirality : 0.041 0.159 3316 Planarity : 0.004 0.043 3920 Dihedral : 5.622 76.618 3044 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.69 % Allowed : 22.28 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.16), residues: 2744 helix: 0.40 (0.12), residues: 1752 sheet: None (None), residues: 0 loop : -2.24 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 129 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.002 PHE D 198 TYR 0.014 0.002 TYR A 413 ARG 0.005 0.001 ARG B 574 Details of bonding type rmsd hydrogen bonds : bond 0.04761 ( 1252) hydrogen bonds : angle 4.16009 ( 3504) covalent geometry : bond 0.00336 (22508) covalent geometry : angle 0.63312 (30460) *********************** 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 214 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 102 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 148 MET cc_start: 0.7021 (pmm) cc_final: 0.6635 (tpp) REVERT: B 173 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8029 (mm-30) REVERT: B 194 MET cc_start: 0.7681 (mmt) cc_final: 0.7276 (mmt) REVERT: B 268 ARG cc_start: 0.6166 (OUTLIER) cc_final: 0.5569 (ptm-80) REVERT: B 480 GLU cc_start: 0.8114 (tt0) cc_final: 0.7806 (mt-10) REVERT: B 591 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: C 183 MET cc_start: 0.8236 (mmm) cc_final: 0.7613 (tmm) REVERT: C 194 MET cc_start: 0.7767 (mmt) cc_final: 0.7406 (mmp) REVERT: C 208 MET cc_start: 0.8823 (mmt) cc_final: 0.8559 (mmm) REVERT: C 256 MET cc_start: 0.6975 (mtt) cc_final: 0.6457 (mmm) REVERT: C 414 ASN cc_start: 0.8449 (OUTLIER) cc_final: 0.7889 (p0) REVERT: C 591 PHE cc_start: 0.8028 (OUTLIER) cc_final: 0.7820 (m-80) REVERT: C 656 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.8110 (tp) REVERT: D 148 MET cc_start: 0.6131 (OUTLIER) cc_final: 0.5529 (mmp) REVERT: D 245 MET cc_start: 0.7620 (mpp) cc_final: 0.7279 (mpp) REVERT: D 321 TRP cc_start: 0.7870 (m100) cc_final: 0.7279 (m100) REVERT: D 632 TRP cc_start: 0.7725 (OUTLIER) cc_final: 0.6628 (t60) REVERT: D 731 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7852 (mp) REVERT: A 292 LYS cc_start: 0.8534 (mttt) cc_final: 0.8276 (mmtm) REVERT: A 321 TRP cc_start: 0.7924 (m100) cc_final: 0.7379 (m100) REVERT: A 353 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7263 (t70) REVERT: A 632 TRP cc_start: 0.7833 (OUTLIER) cc_final: 0.6794 (t60) REVERT: A 687 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8478 (pt) REVERT: A 731 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7708 (mp) outliers start: 112 outliers final: 84 residues processed: 209 average time/residue: 0.2865 time to fit residues: 99.3268 Evaluate side-chains 191 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 94 time to evaluate : 2.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 409 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 542 LEU 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 664 THR Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 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 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 414 ASN 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 591 PHE Chi-restraints excluded: chain C residue 615 ASP Chi-restraints excluded: chain C residue 626 LYS Chi-restraints excluded: chain C residue 656 ILE 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 714 MET 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 177 LEU Chi-restraints excluded: chain D residue 188 HIS Chi-restraints excluded: chain D residue 213 ASP 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 363 VAL 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 512 LEU 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 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 119 ASP 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 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 687 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 767 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 250 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 228 optimal weight: 3.9990 chunk 263 optimal weight: 9.9990 chunk 70 optimal weight: 0.3980 chunk 94 optimal weight: 3.9990 chunk 155 optimal weight: 20.0000 chunk 194 optimal weight: 5.9990 chunk 221 optimal weight: 2.9990 chunk 240 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 243 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.041643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.035059 restraints weight = 235094.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.035984 restraints weight = 119383.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.036600 restraints weight = 75057.216| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 22508 Z= 0.119 Angle : 0.578 12.538 30460 Z= 0.287 Chirality : 0.040 0.151 3316 Planarity : 0.004 0.041 3920 Dihedral : 5.322 76.193 3043 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 4.44 % Allowed : 22.65 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.16), residues: 2744 helix: 0.65 (0.12), residues: 1756 sheet: None (None), residues: 0 loop : -2.14 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 129 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE D 198 TYR 0.012 0.001 TYR B 466 ARG 0.005 0.000 ARG A 114 Details of bonding type rmsd hydrogen bonds : bond 0.04223 ( 1252) hydrogen bonds : angle 3.93443 ( 3504) covalent geometry : bond 0.00256 (22508) covalent geometry : angle 0.57830 (30460) *********************** 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 211 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 105 time to evaluate : 2.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 148 MET cc_start: 0.6959 (pmm) cc_final: 0.6487 (mmp) REVERT: B 173 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7982 (mm-30) REVERT: B 194 MET cc_start: 0.7729 (mmt) cc_final: 0.7376 (mmt) REVERT: B 240 ASP cc_start: 0.8759 (p0) cc_final: 0.8457 (m-30) REVERT: B 245 MET cc_start: 0.7801 (mmm) cc_final: 0.7597 (ptm) REVERT: B 268 ARG cc_start: 0.6213 (OUTLIER) cc_final: 0.5618 (ptm-80) REVERT: B 480 GLU cc_start: 0.8115 (tt0) cc_final: 0.7672 (mt-10) REVERT: B 591 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7789 (m-80) REVERT: B 714 MET cc_start: 0.8506 (tpt) cc_final: 0.8181 (tpp) REVERT: C 183 MET cc_start: 0.8288 (mmm) cc_final: 0.7664 (tmm) REVERT: C 194 MET cc_start: 0.7723 (mmt) cc_final: 0.7380 (mmp) REVERT: C 208 MET cc_start: 0.8822 (mmt) cc_final: 0.8560 (mmm) REVERT: C 256 MET cc_start: 0.6816 (mtt) cc_final: 0.6333 (mmm) REVERT: C 656 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.8098 (tp) REVERT: D 245 MET cc_start: 0.7554 (mpp) cc_final: 0.7160 (mpp) REVERT: D 321 TRP cc_start: 0.7811 (m100) cc_final: 0.7282 (m100) REVERT: D 632 TRP cc_start: 0.7767 (OUTLIER) cc_final: 0.6713 (t60) REVERT: D 731 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7823 (mp) REVERT: A 256 MET cc_start: 0.6250 (tmm) cc_final: 0.5949 (ppp) REVERT: A 292 LYS cc_start: 0.8531 (mttt) cc_final: 0.8268 (mmtm) REVERT: A 321 TRP cc_start: 0.7914 (m100) cc_final: 0.7395 (m100) REVERT: A 353 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7269 (t70) REVERT: A 605 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7113 (pm20) REVERT: A 632 TRP cc_start: 0.7837 (OUTLIER) cc_final: 0.6866 (t60) REVERT: A 731 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7658 (mp) outliers start: 106 outliers final: 75 residues processed: 205 average time/residue: 0.2743 time to fit residues: 94.7319 Evaluate side-chains 181 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 96 time to evaluate : 2.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 409 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 542 LEU 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 703 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 240 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 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 549 ASP Chi-restraints excluded: chain C residue 615 ASP Chi-restraints excluded: chain C residue 626 LYS Chi-restraints excluded: chain C residue 656 ILE 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 714 MET Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 767 ILE 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 363 VAL 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 512 LEU 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 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 158 CYS Chi-restraints excluded: chain A residue 177 LEU Chi-restraints excluded: chain A residue 213 ASP 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 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 687 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 731 LEU 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 128 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 265 optimal weight: 1.9990 chunk 239 optimal weight: 9.9990 chunk 104 optimal weight: 6.9990 chunk 3 optimal weight: 0.0030 chunk 158 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 151 optimal weight: 7.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.041452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.034854 restraints weight = 235131.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.035775 restraints weight = 119924.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.036393 restraints weight = 75712.523| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.4923 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= 0.136 Angle : 0.619 12.004 30460 Z= 0.305 Chirality : 0.041 0.344 3316 Planarity : 0.004 0.039 3920 Dihedral : 5.399 77.213 3040 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.98 % Allowed : 23.12 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.16), residues: 2744 helix: 0.59 (0.12), residues: 1756 sheet: None (None), residues: 0 loop : -2.19 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 129 HIS 0.004 0.001 HIS A 357 PHE 0.012 0.001 PHE D 198 TYR 0.013 0.001 TYR A 413 ARG 0.005 0.001 ARG A 667 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 1252) hydrogen bonds : angle 4.03338 ( 3504) covalent geometry : bond 0.00296 (22508) covalent geometry : angle 0.61915 (30460) *********************** 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 197 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 102 time to evaluate : 2.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 173 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7985 (mm-30) REVERT: B 194 MET cc_start: 0.7735 (mmt) cc_final: 0.7274 (mmt) REVERT: B 240 ASP cc_start: 0.8764 (p0) cc_final: 0.8459 (m-30) REVERT: B 256 MET cc_start: 0.7088 (ptp) cc_final: 0.6492 (tmm) REVERT: B 268 ARG cc_start: 0.6212 (OUTLIER) cc_final: 0.5602 (ptm-80) REVERT: B 480 GLU cc_start: 0.8117 (tt0) cc_final: 0.7828 (mt-10) REVERT: B 714 MET cc_start: 0.8487 (tpt) cc_final: 0.8069 (tpp) REVERT: C 183 MET cc_start: 0.8194 (mmm) cc_final: 0.7709 (tmm) REVERT: C 194 MET cc_start: 0.7764 (mmt) cc_final: 0.7409 (mmp) REVERT: C 208 MET cc_start: 0.8832 (mmt) cc_final: 0.8583 (mmm) REVERT: C 256 MET cc_start: 0.6913 (mtt) cc_final: 0.6371 (mmm) REVERT: C 414 ASN cc_start: 0.8374 (OUTLIER) cc_final: 0.7839 (p0) REVERT: C 656 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.8072 (tp) REVERT: D 147 MET cc_start: 0.7667 (mmm) cc_final: 0.7386 (mmm) REVERT: D 245 MET cc_start: 0.7472 (mpp) cc_final: 0.7061 (mpp) REVERT: D 321 TRP cc_start: 0.7810 (m100) cc_final: 0.7256 (m100) REVERT: D 632 TRP cc_start: 0.7796 (OUTLIER) cc_final: 0.6782 (t60) REVERT: D 731 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7823 (mp) REVERT: A 147 MET cc_start: 0.7461 (mmm) cc_final: 0.7146 (tpt) REVERT: A 148 MET cc_start: 0.6280 (mmp) cc_final: 0.5986 (mmp) REVERT: A 292 LYS cc_start: 0.8534 (mttt) cc_final: 0.8274 (mmtm) REVERT: A 321 TRP cc_start: 0.7921 (m100) cc_final: 0.7284 (m100) REVERT: A 353 ASP cc_start: 0.7926 (OUTLIER) cc_final: 0.7218 (t70) REVERT: A 632 TRP cc_start: 0.7836 (OUTLIER) cc_final: 0.6759 (t60) REVERT: A 731 LEU cc_start: 0.7878 (OUTLIER) cc_final: 0.7636 (mp) outliers start: 95 outliers final: 78 residues processed: 191 average time/residue: 0.2730 time to fit residues: 88.4399 Evaluate side-chains 186 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 99 time to evaluate : 2.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 409 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 656 ILE Chi-restraints excluded: chain B residue 687 LEU Chi-restraints excluded: chain B residue 703 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 240 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 383 VAL Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 414 ASN 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 626 LYS Chi-restraints excluded: chain C residue 656 ILE 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 714 MET Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 767 ILE 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 363 VAL 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 512 LEU 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 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 119 ASP 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 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 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 687 LEU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 767 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 121 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 113 optimal weight: 0.9980 chunk 13 optimal weight: 20.0000 chunk 146 optimal weight: 6.9990 chunk 134 optimal weight: 2.9990 chunk 85 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 157 optimal weight: 9.9990 chunk 246 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 708 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.041976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.035388 restraints weight = 233826.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.036309 restraints weight = 118622.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.036929 restraints weight = 74666.409| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22508 Z= 0.108 Angle : 0.579 11.947 30460 Z= 0.284 Chirality : 0.039 0.272 3316 Planarity : 0.003 0.035 3920 Dihedral : 5.121 76.902 3040 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 3.14 % Allowed : 23.87 % Favored : 72.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2744 helix: 0.87 (0.13), residues: 1756 sheet: None (None), residues: 0 loop : -2.10 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 129 HIS 0.002 0.001 HIS C 357 PHE 0.011 0.001 PHE D 198 TYR 0.010 0.001 TYR A 413 ARG 0.004 0.000 ARG A 667 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 1252) hydrogen bonds : angle 3.83404 ( 3504) covalent geometry : bond 0.00229 (22508) covalent geometry : angle 0.57934 (30460) ********************** 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 184 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 109 time to evaluate : 2.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 173 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7977 (mm-30) REVERT: B 194 MET cc_start: 0.7832 (mmt) cc_final: 0.7358 (mmp) REVERT: B 240 ASP cc_start: 0.8733 (p0) cc_final: 0.8425 (m-30) REVERT: B 256 MET cc_start: 0.6903 (ptp) cc_final: 0.6334 (tmm) REVERT: B 268 ARG cc_start: 0.6289 (OUTLIER) cc_final: 0.5699 (ptm-80) REVERT: B 480 GLU cc_start: 0.8074 (tt0) cc_final: 0.7778 (mt-10) REVERT: B 714 MET cc_start: 0.8478 (tpt) cc_final: 0.8110 (tpp) REVERT: C 183 MET cc_start: 0.8337 (mmm) cc_final: 0.7751 (tmm) REVERT: C 208 MET cc_start: 0.8813 (mmt) cc_final: 0.8557 (mmm) REVERT: C 256 MET cc_start: 0.6933 (mtt) cc_final: 0.6451 (mmm) REVERT: C 656 ILE cc_start: 0.8317 (OUTLIER) cc_final: 0.8062 (tp) REVERT: D 147 MET cc_start: 0.7654 (mmm) cc_final: 0.7317 (mmm) REVERT: D 148 MET cc_start: 0.6188 (mmp) cc_final: 0.5554 (mmp) REVERT: D 245 MET cc_start: 0.7518 (mpp) cc_final: 0.7078 (mpp) REVERT: D 321 TRP cc_start: 0.7816 (m100) cc_final: 0.7351 (m100) REVERT: D 429 VAL cc_start: 0.7769 (OUTLIER) cc_final: 0.7529 (t) REVERT: D 632 TRP cc_start: 0.7817 (OUTLIER) cc_final: 0.6846 (t60) REVERT: A 147 MET cc_start: 0.7431 (mmm) cc_final: 0.7096 (tpt) REVERT: A 148 MET cc_start: 0.6165 (mmp) cc_final: 0.5851 (mmp) REVERT: A 292 LYS cc_start: 0.8504 (mttt) cc_final: 0.8260 (mmtm) REVERT: A 321 TRP cc_start: 0.7799 (m100) cc_final: 0.7246 (m100) REVERT: A 353 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7203 (t70) REVERT: A 632 TRP cc_start: 0.7806 (OUTLIER) cc_final: 0.6890 (t60) REVERT: A 731 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7614 (mp) outliers start: 75 outliers final: 58 residues processed: 180 average time/residue: 0.2795 time to fit residues: 85.1761 Evaluate side-chains 167 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 101 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 173 GLU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 268 ARG 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 542 LEU 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 750 SER Chi-restraints excluded: chain B residue 767 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 240 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 453 LYS 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 626 LYS Chi-restraints excluded: chain C residue 656 ILE Chi-restraints excluded: chain C residue 685 CYS Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 714 MET Chi-restraints excluded: chain C residue 750 SER Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 158 CYS 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 363 VAL 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 512 LEU Chi-restraints excluded: chain D residue 632 TRP 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 158 CYS Chi-restraints excluded: chain A residue 177 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 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 632 TRP Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 664 THR Chi-restraints excluded: chain A residue 687 LEU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 767 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 82 optimal weight: 5.9990 chunk 218 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 166 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 5 optimal weight: 0.5980 chunk 247 optimal weight: 7.9990 chunk 202 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 chunk 183 optimal weight: 6.9990 chunk 159 optimal weight: 0.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 188 HIS D 678 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.041262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.034646 restraints weight = 235548.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.035562 restraints weight = 120516.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.036173 restraints weight = 76149.396| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22508 Z= 0.153 Angle : 0.656 13.028 30460 Z= 0.324 Chirality : 0.041 0.242 3316 Planarity : 0.004 0.041 3920 Dihedral : 5.334 77.974 3036 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.27 % Allowed : 23.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.16), residues: 2744 helix: 0.60 (0.12), residues: 1748 sheet: None (None), residues: 0 loop : -2.10 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 632 HIS 0.006 0.001 HIS C 334 PHE 0.011 0.001 PHE D 198 TYR 0.016 0.002 TYR D 413 ARG 0.005 0.001 ARG A 667 Details of bonding type rmsd hydrogen bonds : bond 0.04582 ( 1252) hydrogen bonds : angle 4.11291 ( 3504) covalent geometry : bond 0.00335 (22508) covalent geometry : angle 0.65555 (30460) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6131.43 seconds wall clock time: 108 minutes 47.71 seconds (6527.71 seconds total)