Starting phenix.real_space_refine on Thu Jun 19 04:30:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i6p_35202/06_2025/8i6p_35202.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i6p_35202/06_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_35202/06_2025/8i6p_35202.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i6p_35202/06_2025/8i6p_35202.map" model { file = "/net/cci-nas-00/data/ceres_data/8i6p_35202/06_2025/8i6p_35202.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i6p_35202/06_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 12.20, per 1000 atoms: 0.55 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: 5.58 Conformation dependent library (CDL) restraints added in 2.9 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: 2.14 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: 6.73 Time building geometry restraints manager: 6.57 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: 0.15 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.850 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 47.460 Find NCS groups from input model: 0.440 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.710 ------------------------------------------------------------------------------- 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 : 2.380 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: 0.3088 time to fit residues: 264.9922 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 : 2.579 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.034089 restraints weight = 236705.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.034995 restraints weight = 122920.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.035595 restraints weight = 78797.271| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 MET cc_start: 0.8394 (mmm) cc_final: 0.7696 (tpp) REVERT: B 194 MET cc_start: 0.7920 (mmt) cc_final: 0.7504 (tpp) REVERT: B 476 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8022 (mp) REVERT: B 480 GLU cc_start: 0.8090 (tt0) cc_final: 0.7808 (mt-10) REVERT: B 541 ASN cc_start: 0.7345 (t0) cc_final: 0.7091 (t0) REVERT: B 549 ASP cc_start: 0.5752 (OUTLIER) cc_final: 0.5098 (p0) REVERT: B 607 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8213 (tp) REVERT: B 734 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: C 183 MET cc_start: 0.8272 (mmm) cc_final: 0.7820 (ppp) REVERT: C 240 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8295 (p0) REVERT: C 256 MET cc_start: 0.7145 (mmm) cc_final: 0.6548 (tmm) REVERT: C 398 PHE cc_start: 0.5973 (m-80) cc_final: 0.5558 (m-80) REVERT: C 400 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7442 (tt) REVERT: C 450 MET cc_start: 0.6144 (mmt) cc_final: 0.5500 (mmt) REVERT: C 476 LEU cc_start: 0.8253 (OUTLIER) cc_final: 0.7769 (mt) REVERT: C 480 GLU cc_start: 0.8121 (tt0) cc_final: 0.7665 (mt-10) REVERT: C 609 SER cc_start: 0.8244 (OUTLIER) cc_final: 0.8039 (m) REVERT: D 123 PHE cc_start: 0.7921 (m-80) cc_final: 0.7313 (m-80) REVERT: D 125 SER cc_start: 0.8028 (OUTLIER) cc_final: 0.7747 (m) REVERT: D 245 MET cc_start: 0.7594 (OUTLIER) cc_final: 0.7378 (mmm) REVERT: D 321 TRP cc_start: 0.7867 (m100) cc_final: 0.7430 (m100) REVERT: D 614 ASP cc_start: 0.6214 (m-30) cc_final: 0.5825 (m-30) REVERT: D 684 CYS cc_start: 0.7498 (m) cc_final: 0.6929 (m) REVERT: A 240 ASP cc_start: 0.7659 (OUTLIER) cc_final: 0.7212 (t0) REVERT: A 321 TRP cc_start: 0.8023 (m100) cc_final: 0.7460 (m100) REVERT: A 335 PHE cc_start: 0.8088 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: A 353 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7479 (t70) REVERT: A 632 TRP cc_start: 0.7633 (OUTLIER) cc_final: 0.7258 (t60) outliers start: 147 outliers final: 78 residues processed: 258 average time/residue: 0.2821 time to fit residues: 122.1045 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 : 2.985 ------------------------------------------------------------------------------- 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: 8.9990 chunk 45 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 231 optimal weight: 9.9990 chunk 259 optimal weight: 0.8980 chunk 190 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 213 optimal weight: 9.9990 chunk 236 optimal weight: 0.8980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 414 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 = 0.3400 r_free = 0.3400 target = 0.041663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.035154 restraints weight = 232697.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.036070 restraints weight = 118568.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.036684 restraints weight = 74829.839| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 22508 Z= 0.111 Angle : 0.548 10.000 30460 Z= 0.278 Chirality : 0.039 0.169 3316 Planarity : 0.003 0.037 3920 Dihedral : 6.163 87.836 3087 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.85 % Allowed : 21.90 % Favored : 74.25 % 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: -0.55 (0.16), residues: 2744 helix: 0.59 (0.12), residues: 1740 sheet: None (None), residues: 0 loop : -2.09 (0.18), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 129 HIS 0.003 0.001 HIS C 168 PHE 0.012 0.001 PHE D 198 TYR 0.011 0.001 TYR D 413 ARG 0.004 0.000 ARG C 348 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 1252) hydrogen bonds : angle 3.94466 ( 3504) covalent geometry : bond 0.00232 (22508) covalent geometry : angle 0.54816 (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 215 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 123 time to evaluate : 2.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 183 MET cc_start: 0.8282 (mmm) cc_final: 0.7610 (tpp) REVERT: B 256 MET cc_start: 0.6364 (tmm) cc_final: 0.6047 (tmm) REVERT: B 340 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7708 (tm-30) REVERT: B 360 ASN cc_start: 0.5529 (OUTLIER) cc_final: 0.5195 (p0) REVERT: B 480 GLU cc_start: 0.7961 (tt0) cc_final: 0.7604 (mm-30) REVERT: B 545 PHE cc_start: 0.5889 (OUTLIER) cc_final: 0.5680 (p90) REVERT: C 183 MET cc_start: 0.8147 (mmm) cc_final: 0.7618 (tmm) REVERT: C 256 MET cc_start: 0.7094 (mmm) cc_final: 0.6365 (tmm) REVERT: C 400 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7469 (tt) REVERT: C 468 MET cc_start: 0.7659 (ttm) cc_final: 0.7397 (tpp) REVERT: C 480 GLU cc_start: 0.8003 (tt0) cc_final: 0.7749 (mm-30) REVERT: D 123 PHE cc_start: 0.8019 (m-80) cc_final: 0.7515 (m-80) REVERT: D 183 MET cc_start: 0.7084 (mmm) cc_final: 0.6721 (ppp) REVERT: D 245 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.7290 (mmm) REVERT: D 321 TRP cc_start: 0.7728 (m100) cc_final: 0.7430 (m100) REVERT: D 480 GLU cc_start: 0.8260 (tm-30) cc_final: 0.8057 (tm-30) REVERT: D 614 ASP cc_start: 0.6186 (m-30) cc_final: 0.5846 (m-30) REVERT: D 684 CYS cc_start: 0.7446 (m) cc_final: 0.6981 (m) REVERT: A 321 TRP cc_start: 0.7993 (m100) cc_final: 0.7447 (m100) REVERT: A 353 ASP cc_start: 0.8008 (OUTLIER) cc_final: 0.7534 (t70) REVERT: A 632 TRP cc_start: 0.7639 (OUTLIER) cc_final: 0.7271 (t60) outliers start: 92 outliers final: 53 residues processed: 209 average time/residue: 0.2942 time to fit residues: 101.8948 Evaluate side-chains 163 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 103 time to evaluate : 2.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 429 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 632 TRP Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 675 GLN 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 337 SER Chi-restraints excluded: chain C residue 351 THR 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 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 767 ILE Chi-restraints excluded: chain D residue 158 CYS 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 429 VAL Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 767 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 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 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: 10.0000 chunk 102 optimal weight: 0.4980 chunk 17 optimal weight: 0.0970 chunk 226 optimal weight: 8.9990 chunk 96 optimal weight: 10.0000 chunk 181 optimal weight: 5.9990 chunk 248 optimal weight: 5.9990 chunk 37 optimal weight: 20.0000 chunk 254 optimal weight: 9.9990 chunk 227 optimal weight: 0.0570 chunk 206 optimal weight: 9.9990 overall best weight: 2.5300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.041304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.034774 restraints weight = 236405.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.035695 restraints weight = 119700.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.036305 restraints weight = 75265.748| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22508 Z= 0.124 Angle : 0.567 11.051 30460 Z= 0.285 Chirality : 0.039 0.160 3316 Planarity : 0.004 0.035 3920 Dihedral : 5.458 80.746 3052 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.02 % Allowed : 21.69 % Favored : 74.29 % 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: -0.46 (0.16), residues: 2744 helix: 0.67 (0.12), residues: 1744 sheet: None (None), residues: 0 loop : -2.08 (0.17), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 129 HIS 0.004 0.001 HIS C 334 PHE 0.011 0.001 PHE D 198 TYR 0.014 0.001 TYR D 413 ARG 0.010 0.000 ARG B 348 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 1252) hydrogen bonds : angle 3.92960 ( 3504) covalent geometry : bond 0.00267 (22508) covalent geometry : angle 0.56725 (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 213 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 117 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.7940 (mmt) cc_final: 0.7348 (mmp) REVERT: B 245 MET cc_start: 0.7748 (tpp) cc_final: 0.7070 (ptm) REVERT: B 360 ASN cc_start: 0.5606 (OUTLIER) cc_final: 0.5264 (p0) REVERT: B 480 GLU cc_start: 0.7974 (tt0) cc_final: 0.7684 (mt-10) REVERT: B 545 PHE cc_start: 0.5820 (OUTLIER) cc_final: 0.5619 (p90) REVERT: C 183 MET cc_start: 0.8137 (mmm) cc_final: 0.7560 (tmm) REVERT: C 194 MET cc_start: 0.7790 (mmt) cc_final: 0.7431 (mmp) REVERT: C 400 LEU cc_start: 0.7608 (OUTLIER) cc_final: 0.7377 (tt) REVERT: C 545 PHE cc_start: 0.6228 (OUTLIER) cc_final: 0.5948 (p90) REVERT: D 114 ARG cc_start: 0.6138 (OUTLIER) cc_final: 0.5828 (ttm-80) REVERT: D 123 PHE cc_start: 0.8159 (m-80) cc_final: 0.7616 (m-80) REVERT: D 321 TRP cc_start: 0.7727 (m100) cc_final: 0.7338 (m100) REVERT: D 445 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7507 (ttm170) REVERT: D 480 GLU cc_start: 0.8239 (tm-30) cc_final: 0.8024 (tm-30) REVERT: D 684 CYS cc_start: 0.7456 (m) cc_final: 0.6894 (m) REVERT: A 147 MET cc_start: 0.7380 (mmm) cc_final: 0.7072 (mmm) REVERT: A 321 TRP cc_start: 0.7968 (m100) cc_final: 0.7400 (m100) REVERT: A 353 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7525 (t70) REVERT: A 632 TRP cc_start: 0.7683 (OUTLIER) cc_final: 0.7181 (t60) outliers start: 96 outliers final: 61 residues processed: 209 average time/residue: 0.2887 time to fit residues: 98.9973 Evaluate side-chains 170 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 101 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 399 CYS Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 429 VAL Chi-restraints excluded: chain B residue 542 LEU Chi-restraints excluded: chain B residue 545 PHE Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 687 LEU 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 146 PHE Chi-restraints excluded: chain C residue 173 GLU 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 400 LEU Chi-restraints excluded: chain C residue 409 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 615 ASP Chi-restraints excluded: chain C residue 664 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 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 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 445 ARG 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 767 ILE 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 687 LEU Chi-restraints excluded: chain A residue 767 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 196 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 34 optimal weight: 10.0000 chunk 213 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 48 optimal weight: 0.0470 chunk 54 optimal weight: 0.8980 chunk 160 optimal weight: 3.9990 chunk 265 optimal weight: 2.9990 overall best weight: 1.3884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.041962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.035465 restraints weight = 232063.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.036399 restraints weight = 117624.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.037004 restraints weight = 73741.034| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22508 Z= 0.102 Angle : 0.524 10.696 30460 Z= 0.263 Chirality : 0.039 0.153 3316 Planarity : 0.003 0.030 3920 Dihedral : 4.904 78.995 3042 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.94 % Allowed : 21.27 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.08 (0.16), residues: 2744 helix: 0.95 (0.13), residues: 1744 sheet: None (None), residues: 0 loop : -1.88 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 129 HIS 0.003 0.001 HIS A 357 PHE 0.012 0.001 PHE D 198 TYR 0.014 0.001 TYR C 466 ARG 0.007 0.000 ARG D 185 Details of bonding type rmsd hydrogen bonds : bond 0.03756 ( 1252) hydrogen bonds : angle 3.73463 ( 3504) covalent geometry : bond 0.00214 (22508) covalent geometry : angle 0.52378 (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 213 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 119 time to evaluate : 2.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.7951 (mmt) cc_final: 0.7349 (mmp) REVERT: B 256 MET cc_start: 0.6373 (tmm) cc_final: 0.6090 (tmm) REVERT: B 468 MET cc_start: 0.7343 (tpp) cc_final: 0.7065 (tpp) REVERT: B 480 GLU cc_start: 0.7970 (tt0) cc_final: 0.7727 (mm-30) REVERT: B 545 PHE cc_start: 0.5740 (OUTLIER) cc_final: 0.5529 (p90) REVERT: C 183 MET cc_start: 0.8119 (mmm) cc_final: 0.7487 (tmm) REVERT: C 194 MET cc_start: 0.7811 (mmt) cc_final: 0.7376 (mmp) REVERT: C 468 MET cc_start: 0.7711 (ttm) cc_final: 0.7407 (tpp) REVERT: C 545 PHE cc_start: 0.6196 (OUTLIER) cc_final: 0.5873 (p90) REVERT: D 123 PHE cc_start: 0.8141 (m-80) cc_final: 0.7552 (m-80) REVERT: D 125 SER cc_start: 0.7844 (OUTLIER) cc_final: 0.7556 (m) REVERT: D 147 MET cc_start: 0.8013 (mmt) cc_final: 0.7510 (tpp) REVERT: D 183 MET cc_start: 0.6789 (mmm) cc_final: 0.6515 (ppp) REVERT: D 321 TRP cc_start: 0.7759 (m100) cc_final: 0.7406 (m100) REVERT: D 445 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7507 (ptm160) REVERT: D 480 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8184 (tm-30) REVERT: D 684 CYS cc_start: 0.7471 (m) cc_final: 0.7022 (m) REVERT: A 292 LYS cc_start: 0.8413 (mttt) cc_final: 0.8095 (mmtm) REVERT: A 321 TRP cc_start: 0.8089 (m100) cc_final: 0.7580 (m100) REVERT: A 335 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7311 (m-80) outliers start: 94 outliers final: 54 residues processed: 208 average time/residue: 0.3093 time to fit residues: 105.2624 Evaluate side-chains 162 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 103 time to evaluate : 2.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 545 PHE Chi-restraints excluded: chain B residue 549 ASP Chi-restraints excluded: chain B residue 615 ASP Chi-restraints excluded: chain B residue 632 TRP Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 687 LEU 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 146 PHE Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 545 PHE 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 750 SER Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 125 SER Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 445 ARG Chi-restraints excluded: chain D residue 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 767 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 257 VAL 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 363 VAL Chi-restraints excluded: chain A residue 387 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 663 LEU Chi-restraints excluded: chain A residue 687 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: 20.0000 chunk 270 optimal weight: 4.9990 chunk 203 optimal weight: 6.9990 chunk 262 optimal weight: 4.9990 chunk 227 optimal weight: 9.9990 chunk 36 optimal weight: 6.9990 chunk 233 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 265 optimal weight: 0.5980 chunk 169 optimal weight: 0.0970 chunk 151 optimal weight: 4.9990 overall best weight: 3.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 180 GLN ** D 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.041183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.034702 restraints weight = 235538.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.035620 restraints weight = 119099.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.036223 restraints weight = 75098.424| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.4170 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= 0.136 Angle : 0.595 10.676 30460 Z= 0.295 Chirality : 0.040 0.153 3316 Planarity : 0.004 0.036 3920 Dihedral : 4.974 76.360 3032 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.98 % Allowed : 22.32 % 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: -0.36 (0.16), residues: 2744 helix: 0.76 (0.12), residues: 1744 sheet: None (None), residues: 0 loop : -2.06 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 628 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE D 198 TYR 0.014 0.001 TYR A 413 ARG 0.008 0.001 ARG D 185 Details of bonding type rmsd hydrogen bonds : bond 0.04350 ( 1252) hydrogen bonds : angle 3.92821 ( 3504) covalent geometry : bond 0.00296 (22508) covalent geometry : angle 0.59505 (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 197 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 102 time to evaluate : 2.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.7844 (mmt) cc_final: 0.7296 (mmp) REVERT: B 245 MET cc_start: 0.7614 (mmm) cc_final: 0.7384 (ptm) REVERT: B 256 MET cc_start: 0.6258 (tmm) cc_final: 0.6002 (tmm) REVERT: B 360 ASN cc_start: 0.5937 (OUTLIER) cc_final: 0.5079 (p0) REVERT: B 480 GLU cc_start: 0.7961 (tt0) cc_final: 0.7719 (mt-10) REVERT: B 591 PHE cc_start: 0.7911 (OUTLIER) cc_final: 0.7676 (m-80) REVERT: C 183 MET cc_start: 0.8143 (mmm) cc_final: 0.7590 (tmm) REVERT: C 194 MET cc_start: 0.7804 (mmt) cc_final: 0.7376 (mmp) REVERT: C 591 PHE cc_start: 0.7834 (OUTLIER) cc_final: 0.7452 (m-80) REVERT: D 123 PHE cc_start: 0.8271 (m-80) cc_final: 0.7614 (m-80) REVERT: D 125 SER cc_start: 0.7825 (OUTLIER) cc_final: 0.7506 (m) REVERT: D 147 MET cc_start: 0.7978 (mmt) cc_final: 0.7655 (tpp) REVERT: D 321 TRP cc_start: 0.7877 (m100) cc_final: 0.7433 (m100) REVERT: D 445 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7482 (ttm170) REVERT: D 468 MET cc_start: 0.6867 (ptm) cc_final: 0.6423 (ptt) REVERT: D 684 CYS cc_start: 0.7470 (m) cc_final: 0.6893 (m) REVERT: A 292 LYS cc_start: 0.8546 (mttt) cc_final: 0.8262 (mmtm) REVERT: A 321 TRP cc_start: 0.7950 (m100) cc_final: 0.7345 (m100) REVERT: A 353 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7340 (t70) REVERT: A 605 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.6716 (pm20) outliers start: 95 outliers final: 66 residues processed: 193 average time/residue: 0.3245 time to fit residues: 103.2681 Evaluate side-chains 171 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 98 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 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 538 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 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 767 ILE Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 173 GLU Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 409 VAL Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 589 SER Chi-restraints excluded: chain C residue 591 PHE Chi-restraints excluded: chain C residue 615 ASP Chi-restraints excluded: chain C residue 626 LYS Chi-restraints excluded: chain C residue 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 125 SER 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 213 ASP Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 387 VAL Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 429 VAL Chi-restraints excluded: chain D residue 445 ARG 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 683 ILE Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 767 ILE Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 114 ARG Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 158 CYS Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 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 512 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 687 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: 3.9990 chunk 7 optimal weight: 6.9990 chunk 112 optimal weight: 5.9990 chunk 177 optimal weight: 20.0000 chunk 267 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 52 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 675 GLN ** D 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.041305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.034758 restraints weight = 234556.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.035682 restraints weight = 119459.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.036292 restraints weight = 75390.166| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4446 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= 0.133 Angle : 0.585 10.218 30460 Z= 0.291 Chirality : 0.040 0.170 3316 Planarity : 0.004 0.037 3920 Dihedral : 4.914 73.812 3031 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.89 % Allowed : 22.24 % Favored : 73.87 % 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: -0.38 (0.16), residues: 2744 helix: 0.74 (0.12), residues: 1744 sheet: None (None), residues: 0 loop : -2.07 (0.18), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 632 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE D 198 TYR 0.014 0.001 TYR D 413 ARG 0.007 0.001 ARG D 185 Details of bonding type rmsd hydrogen bonds : bond 0.04293 ( 1252) hydrogen bonds : angle 3.94695 ( 3504) covalent geometry : bond 0.00290 (22508) covalent geometry : angle 0.58530 (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 199 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 106 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.7862 (mmt) cc_final: 0.7428 (mmp) REVERT: B 240 ASP cc_start: 0.8726 (p0) cc_final: 0.8472 (m-30) REVERT: B 245 MET cc_start: 0.7760 (mmm) cc_final: 0.7530 (ptm) REVERT: B 256 MET cc_start: 0.6538 (tmm) cc_final: 0.6326 (tmm) REVERT: B 468 MET cc_start: 0.7118 (tpp) cc_final: 0.6911 (tpp) REVERT: B 480 GLU cc_start: 0.8046 (tt0) cc_final: 0.7780 (mt-10) REVERT: B 591 PHE cc_start: 0.7927 (OUTLIER) cc_final: 0.7725 (m-80) REVERT: C 183 MET cc_start: 0.8142 (mmm) cc_final: 0.7576 (tmm) REVERT: C 194 MET cc_start: 0.7780 (mmt) cc_final: 0.7416 (mmm) REVERT: C 208 MET cc_start: 0.8799 (mmt) cc_final: 0.8530 (mmm) REVERT: C 297 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8563 (mp) REVERT: D 125 SER cc_start: 0.7828 (OUTLIER) cc_final: 0.7622 (m) REVERT: D 321 TRP cc_start: 0.7950 (m100) cc_final: 0.7460 (m100) REVERT: D 684 CYS cc_start: 0.7518 (m) cc_final: 0.6977 (m) REVERT: A 292 LYS cc_start: 0.8564 (mttt) cc_final: 0.8302 (mmtm) REVERT: A 321 TRP cc_start: 0.7969 (m100) cc_final: 0.7379 (m100) REVERT: A 353 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7342 (t70) REVERT: A 605 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.6821 (pm20) outliers start: 93 outliers final: 71 residues processed: 194 average time/residue: 0.2893 time to fit residues: 93.9908 Evaluate side-chains 175 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 99 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 ASN Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 248 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 360 ASN Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 383 VAL Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 538 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 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 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 297 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 409 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 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 125 SER 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 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 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 683 ILE Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain D residue 767 ILE 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 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 512 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 687 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: 5.9990 chunk 76 optimal weight: 6.9990 chunk 228 optimal weight: 6.9990 chunk 263 optimal weight: 7.9990 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 221 optimal weight: 0.9980 chunk 240 optimal weight: 8.9990 chunk 111 optimal weight: 9.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 715 GLN C 442 GLN ** D 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.040740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.034161 restraints weight = 238447.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.035084 restraints weight = 121860.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.035683 restraints weight = 77272.115| |-----------------------------------------------------------------------------| r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.4756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 22508 Z= 0.188 Angle : 0.685 11.228 30460 Z= 0.342 Chirality : 0.043 0.284 3316 Planarity : 0.005 0.045 3920 Dihedral : 5.297 75.813 3030 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.27 % Allowed : 21.78 % Favored : 73.95 % 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: -0.85 (0.15), residues: 2744 helix: 0.32 (0.12), residues: 1748 sheet: None (None), residues: 0 loop : -2.15 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 129 HIS 0.008 0.002 HIS A 357 PHE 0.012 0.002 PHE D 198 TYR 0.022 0.002 TYR A 484 ARG 0.007 0.001 ARG D 652 Details of bonding type rmsd hydrogen bonds : bond 0.05036 ( 1252) hydrogen bonds : angle 4.30658 ( 3504) covalent geometry : bond 0.00411 (22508) covalent geometry : angle 0.68452 (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 210 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 108 time to evaluate : 2.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.7725 (mmt) cc_final: 0.7376 (mmt) REVERT: B 245 MET cc_start: 0.7813 (mmm) cc_final: 0.7606 (ptm) REVERT: B 256 MET cc_start: 0.6298 (tmm) cc_final: 0.6087 (tmm) REVERT: B 480 GLU cc_start: 0.8018 (tt0) cc_final: 0.7755 (mt-10) REVERT: B 591 PHE cc_start: 0.7923 (OUTLIER) cc_final: 0.7671 (m-80) REVERT: C 194 MET cc_start: 0.7723 (mmt) cc_final: 0.7422 (mmm) REVERT: C 256 MET cc_start: 0.7058 (mtt) cc_final: 0.5904 (tmm) REVERT: C 297 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8533 (mp) REVERT: C 656 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.8096 (tp) REVERT: D 125 SER cc_start: 0.7815 (OUTLIER) cc_final: 0.7592 (m) REVERT: D 321 TRP cc_start: 0.7781 (m100) cc_final: 0.7149 (m100) REVERT: D 632 TRP cc_start: 0.7679 (OUTLIER) cc_final: 0.6658 (t60) REVERT: D 684 CYS cc_start: 0.7559 (m) cc_final: 0.6999 (m) REVERT: D 731 LEU cc_start: 0.8039 (OUTLIER) cc_final: 0.7833 (mp) REVERT: A 292 LYS cc_start: 0.8533 (mttt) cc_final: 0.8280 (mmtm) REVERT: A 321 TRP cc_start: 0.7896 (m100) cc_final: 0.7230 (m100) REVERT: A 353 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7202 (t70) REVERT: A 605 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6688 (pm20) REVERT: A 687 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8481 (pt) outliers start: 102 outliers final: 73 residues processed: 205 average time/residue: 0.2917 time to fit residues: 98.3767 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 : 2.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 ASN 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 538 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 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 83 MET 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 297 LEU 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 409 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 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 125 SER 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 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 445 ARG 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 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 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 512 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 683 ILE Chi-restraints excluded: chain A residue 687 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: 0.9990 chunk 13 optimal weight: 3.9990 chunk 81 optimal weight: 0.2980 chunk 85 optimal weight: 0.0270 chunk 265 optimal weight: 9.9990 chunk 239 optimal weight: 0.7980 chunk 104 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 chunk 151 optimal weight: 6.9990 overall best weight: 0.6240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 401 HIS A 401 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.042124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.035623 restraints weight = 231145.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.036544 restraints weight = 117297.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.037164 restraints weight = 73642.823| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22508 Z= 0.107 Angle : 0.572 11.540 30460 Z= 0.279 Chirality : 0.040 0.227 3316 Planarity : 0.004 0.087 3920 Dihedral : 4.737 74.100 3030 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.39 % Allowed : 23.37 % Favored : 74.25 % 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: -0.16 (0.16), residues: 2744 helix: 0.91 (0.13), residues: 1752 sheet: None (None), residues: 0 loop : -2.00 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 129 HIS 0.002 0.001 HIS C 357 PHE 0.011 0.001 PHE D 522 TYR 0.010 0.001 TYR B 413 ARG 0.013 0.000 ARG D 539 Details of bonding type rmsd hydrogen bonds : bond 0.03821 ( 1252) hydrogen bonds : angle 3.77729 ( 3504) covalent geometry : bond 0.00222 (22508) covalent geometry : angle 0.57199 (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 178 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 121 time to evaluate : 2.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 194 MET cc_start: 0.7889 (mmt) cc_final: 0.7474 (mmp) REVERT: B 245 MET cc_start: 0.7689 (mmm) cc_final: 0.7459 (ptm) REVERT: B 256 MET cc_start: 0.6639 (tmm) cc_final: 0.6421 (tmm) REVERT: C 194 MET cc_start: 0.7801 (mmt) cc_final: 0.7442 (mmm) REVERT: C 208 MET cc_start: 0.8790 (mmt) cc_final: 0.8517 (mmm) REVERT: C 256 MET cc_start: 0.7149 (mtt) cc_final: 0.6666 (mmm) REVERT: C 297 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8491 (mp) REVERT: C 468 MET cc_start: 0.7893 (ttm) cc_final: 0.7465 (mmt) REVERT: C 541 ASN cc_start: 0.7015 (t0) cc_final: 0.6759 (t0) REVERT: D 321 TRP cc_start: 0.7875 (m100) cc_final: 0.7358 (m100) REVERT: D 429 VAL cc_start: 0.7688 (OUTLIER) cc_final: 0.7444 (t) REVERT: D 632 TRP cc_start: 0.7806 (OUTLIER) cc_final: 0.6879 (t60) REVERT: A 148 MET cc_start: 0.6285 (mmp) cc_final: 0.6080 (mmp) REVERT: A 292 LYS cc_start: 0.8486 (mttt) cc_final: 0.8231 (mmtm) REVERT: A 321 TRP cc_start: 0.7753 (m100) cc_final: 0.7184 (m100) REVERT: A 468 MET cc_start: 0.7409 (tmm) cc_final: 0.6898 (ppp) REVERT: A 605 GLU cc_start: 0.8021 (OUTLIER) cc_final: 0.6990 (pm20) outliers start: 57 outliers final: 36 residues processed: 174 average time/residue: 0.3024 time to fit residues: 88.1618 Evaluate side-chains 141 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 101 time to evaluate : 2.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 229 GLU Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 538 LEU 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 750 SER Chi-restraints excluded: chain C residue 146 PHE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 494 VAL Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 703 VAL Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain D residue 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 735 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 177 LEU 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 387 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 663 LEU Chi-restraints excluded: chain A residue 687 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: 9.9990 chunk 11 optimal weight: 5.9990 chunk 113 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 134 optimal weight: 0.7980 chunk 85 optimal weight: 0.7980 chunk 54 optimal weight: 3.9990 chunk 157 optimal weight: 0.0070 chunk 246 optimal weight: 0.3980 chunk 47 optimal weight: 0.0570 overall best weight: 0.4116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 551 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.042520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.035952 restraints weight = 232142.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.036882 restraints weight = 117274.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.037502 restraints weight = 73775.982| |-----------------------------------------------------------------------------| r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.4983 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 22508 Z= 0.102 Angle : 0.560 13.317 30460 Z= 0.273 Chirality : 0.039 0.215 3316 Planarity : 0.003 0.069 3920 Dihedral : 4.445 74.630 3027 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.55 % Allowed : 24.33 % Favored : 74.12 % 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: 0.05 (0.16), residues: 2744 helix: 1.08 (0.13), residues: 1748 sheet: None (None), residues: 0 loop : -1.91 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 129 HIS 0.002 0.000 HIS A 501 PHE 0.010 0.001 PHE D 522 TYR 0.012 0.001 TYR B 413 ARG 0.013 0.000 ARG D 539 Details of bonding type rmsd hydrogen bonds : bond 0.03530 ( 1252) hydrogen bonds : angle 3.66375 ( 3504) covalent geometry : bond 0.00211 (22508) covalent geometry : angle 0.56031 (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 147 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 110 time to evaluate : 3.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 245 MET cc_start: 0.7667 (mmm) cc_final: 0.7413 (ptm) REVERT: B 256 MET cc_start: 0.6512 (tmm) cc_final: 0.6285 (tmm) REVERT: B 468 MET cc_start: 0.7317 (tpp) cc_final: 0.7009 (ttt) REVERT: C 194 MET cc_start: 0.7856 (mmt) cc_final: 0.7419 (mmm) REVERT: C 208 MET cc_start: 0.8759 (mmt) cc_final: 0.8500 (mmm) REVERT: C 468 MET cc_start: 0.7874 (ttm) cc_final: 0.7417 (mmt) REVERT: C 541 ASN cc_start: 0.7061 (t0) cc_final: 0.6796 (t0) REVERT: D 147 MET cc_start: 0.7446 (mmm) cc_final: 0.7212 (tpt) REVERT: D 321 TRP cc_start: 0.7852 (m100) cc_final: 0.7402 (m100) REVERT: D 632 TRP cc_start: 0.7756 (OUTLIER) cc_final: 0.6934 (t60) REVERT: A 147 MET cc_start: 0.7560 (mmm) cc_final: 0.7188 (mmm) REVERT: A 148 MET cc_start: 0.6131 (mmp) cc_final: 0.5683 (mmp) REVERT: A 292 LYS cc_start: 0.8462 (mttt) cc_final: 0.8200 (mmtm) REVERT: A 321 TRP cc_start: 0.7861 (m100) cc_final: 0.7322 (m100) REVERT: A 468 MET cc_start: 0.7421 (tmm) cc_final: 0.6830 (ppp) REVERT: A 605 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7027 (pm20) REVERT: A 687 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8281 (tt) outliers start: 37 outliers final: 31 residues processed: 147 average time/residue: 0.3097 time to fit residues: 77.6389 Evaluate side-chains 133 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 2.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 409 VAL Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 538 LEU 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 146 PHE Chi-restraints excluded: chain C residue 240 ASP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 549 ASP Chi-restraints excluded: chain C residue 767 ILE Chi-restraints excluded: chain D residue 158 CYS Chi-restraints excluded: chain D residue 270 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 409 VAL Chi-restraints excluded: chain D residue 553 THR Chi-restraints excluded: chain D residue 632 TRP Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain D residue 735 THR Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 177 LEU 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 512 LEU Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 605 GLU Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 687 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: 0.0870 chunk 218 optimal weight: 7.9990 chunk 68 optimal weight: 20.0000 chunk 166 optimal weight: 0.0770 chunk 85 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 247 optimal weight: 6.9990 chunk 202 optimal weight: 8.9990 chunk 142 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 overall best weight: 3.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 188 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.041229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.034618 restraints weight = 234021.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.035541 restraints weight = 119428.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.036138 restraints weight = 75751.212| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22508 Z= 0.153 Angle : 0.646 11.720 30460 Z= 0.320 Chirality : 0.041 0.198 3316 Planarity : 0.004 0.066 3920 Dihedral : 4.865 76.530 3026 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.05 % Allowed : 24.12 % Favored : 73.83 % 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: -0.38 (0.16), residues: 2744 helix: 0.71 (0.12), residues: 1748 sheet: None (None), residues: 0 loop : -2.00 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 129 HIS 0.007 0.001 HIS A 357 PHE 0.011 0.002 PHE A 763 TYR 0.016 0.002 TYR A 484 ARG 0.012 0.001 ARG D 539 Details of bonding type rmsd hydrogen bonds : bond 0.04573 ( 1252) hydrogen bonds : angle 4.03468 ( 3504) covalent geometry : bond 0.00337 (22508) covalent geometry : angle 0.64551 (30460) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6797.97 seconds wall clock time: 121 minutes 19.82 seconds (7279.82 seconds total)