Starting phenix.real_space_refine on Mon May 4 15:03:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iqx_60797/05_2026/9iqx_60797_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iqx_60797/05_2026/9iqx_60797.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iqx_60797/05_2026/9iqx_60797_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iqx_60797/05_2026/9iqx_60797_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iqx_60797/05_2026/9iqx_60797.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iqx_60797/05_2026/9iqx_60797.map" } resolution = 3.37 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.066 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 118 5.16 5 C 14438 2.51 5 N 3694 2.21 5 O 4008 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22266 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 4830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 600, 4830 Classifications: {'peptide': 600} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 577} Chain breaks: 2 Chain: "D" Number of atoms: 4870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 605, 4870 Classifications: {'peptide': 605} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 581} Chain breaks: 2 Chain: "E" Number of atoms: 1360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1360 Classifications: {'peptide': 180} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 11, 'TRANS': 168} Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 79 Unresolved non-hydrogen dihedrals: 53 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 44 Unusual residues: {'U6L': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: A, B, F Time building chain proxies: 7.10, per 1000 atoms: 0.32 Number of scatterers: 22266 At special positions: 0 Unit cell: (171.72, 180.36, 122.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 118 16.00 P 6 15.00 Mg 2 11.99 O 4008 8.00 N 3694 7.00 C 14438 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS C 639 " - pdb=" SG CYS C 660 " distance=2.03 Simple disulfide: pdb=" SG CYS D 639 " - pdb=" SG CYS D 660 " distance=2.03 Simple disulfide: pdb=" SG CYS A 639 " - pdb=" SG CYS A 660 " distance=2.03 Simple disulfide: pdb=" SG CYS B 639 " - pdb=" SG CYS B 660 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 1.0 seconds 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5240 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 6 sheets defined 64.9% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'C' and resid 150 through 161 Processing helix chain 'C' and resid 163 through 176 Proline residue: C 171 - end of helix Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.640A pdb=" N LYS C 197 " --> pdb=" O THR C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 221 Processing helix chain 'C' and resid 222 through 228 Processing helix chain 'C' and resid 240 through 248 Processing helix chain 'C' and resid 250 through 261 Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 287 through 295 Processing helix chain 'C' and resid 297 through 306 Processing helix chain 'C' and resid 323 through 332 Processing helix chain 'C' and resid 335 through 357 Processing helix chain 'C' and resid 361 through 365 Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 382 through 391 Processing helix chain 'C' and resid 432 through 439 Processing helix chain 'C' and resid 444 through 450 removed outlier: 4.177A pdb=" N GLU C 448 " --> pdb=" O GLU C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 467 Processing helix chain 'C' and resid 467 through 491 Processing helix chain 'C' and resid 504 through 530 Processing helix chain 'C' and resid 550 through 570 Processing helix chain 'C' and resid 573 through 591 removed outlier: 3.799A pdb=" N VAL C 577 " --> pdb=" O ALA C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 637 removed outlier: 3.958A pdb=" N PHE C 615 " --> pdb=" O PHE C 611 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG C 616 " --> pdb=" O LYS C 612 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 620 " --> pdb=" O ARG C 616 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR C 621 " --> pdb=" O PHE C 617 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER C 634 " --> pdb=" O SER C 630 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU C 635 " --> pdb=" O ALA C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 662 through 679 Processing helix chain 'C' and resid 684 through 688 Processing helix chain 'C' and resid 691 through 724 removed outlier: 3.721A pdb=" N PHE C 695 " --> pdb=" O TYR C 691 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU C 717 " --> pdb=" O MET C 713 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 748 removed outlier: 3.506A pdb=" N PHE C 748 " --> pdb=" O ILE C 744 " (cutoff:3.500A) Processing helix chain 'C' and resid 749 through 756 Processing helix chain 'D' and resid 150 through 161 removed outlier: 3.651A pdb=" N ASP D 156 " --> pdb=" O PRO D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 167 No H-bonds generated for 'chain 'D' and resid 165 through 167' Processing helix chain 'D' and resid 168 through 177 Processing helix chain 'D' and resid 182 through 186 Processing helix chain 'D' and resid 193 through 199 removed outlier: 3.589A pdb=" N LYS D 197 " --> pdb=" O THR D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 221 removed outlier: 3.973A pdb=" N VAL D 212 " --> pdb=" O ASP D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 228 Processing helix chain 'D' and resid 240 through 248 removed outlier: 3.912A pdb=" N ILE D 244 " --> pdb=" O THR D 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 261 Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 287 through 295 Processing helix chain 'D' and resid 297 through 306 Processing helix chain 'D' and resid 323 through 331 Processing helix chain 'D' and resid 335 through 357 removed outlier: 4.264A pdb=" N PHE D 341 " --> pdb=" O GLU D 337 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR D 343 " --> pdb=" O THR D 339 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS D 344 " --> pdb=" O LYS D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 365 removed outlier: 3.951A pdb=" N VAL D 365 " --> pdb=" O LEU D 362 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 382 through 391 Processing helix chain 'D' and resid 399 through 403 removed outlier: 3.850A pdb=" N LEU D 402 " --> pdb=" O THR D 399 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER D 403 " --> pdb=" O ARG D 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 399 through 403' Processing helix chain 'D' and resid 432 through 439 Processing helix chain 'D' and resid 445 through 451 Processing helix chain 'D' and resid 452 through 466 Processing helix chain 'D' and resid 466 through 492 Processing helix chain 'D' and resid 504 through 532 Processing helix chain 'D' and resid 549 through 570 Processing helix chain 'D' and resid 573 through 589 Processing helix chain 'D' and resid 590 through 594 Processing helix chain 'D' and resid 596 through 605 removed outlier: 4.588A pdb=" N THR D 601 " --> pdb=" O LYS D 597 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N TYR D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N MET D 605 " --> pdb=" O THR D 601 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 634 removed outlier: 3.953A pdb=" N PHE D 611 " --> pdb=" O GLN D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 664 through 679 removed outlier: 3.722A pdb=" N THR D 668 " --> pdb=" O GLU D 664 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 689 removed outlier: 4.045A pdb=" N SER D 688 " --> pdb=" O GLU D 684 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR D 689 " --> pdb=" O MET D 685 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 684 through 689' Processing helix chain 'D' and resid 691 through 723 Processing helix chain 'D' and resid 725 through 747 removed outlier: 4.819A pdb=" N TRP D 733 " --> pdb=" O SER D 729 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYS D 734 " --> pdb=" O LYS D 730 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU D 735 " --> pdb=" O HIS D 731 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 756 Processing helix chain 'A' and resid 151 through 161 Processing helix chain 'A' and resid 163 through 176 Proline residue: A 171 - end of helix Processing helix chain 'A' and resid 193 through 201 removed outlier: 3.640A pdb=" N LYS A 197 " --> pdb=" O THR A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 221 Processing helix chain 'A' and resid 222 through 228 Processing helix chain 'A' and resid 240 through 248 Processing helix chain 'A' and resid 250 through 261 Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 297 through 306 Processing helix chain 'A' and resid 323 through 332 Processing helix chain 'A' and resid 335 through 357 Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 382 through 391 Processing helix chain 'A' and resid 432 through 439 Processing helix chain 'A' and resid 444 through 450 removed outlier: 4.177A pdb=" N GLU A 448 " --> pdb=" O GLU A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 467 Processing helix chain 'A' and resid 467 through 491 Processing helix chain 'A' and resid 504 through 530 Processing helix chain 'A' and resid 550 through 570 Processing helix chain 'A' and resid 573 through 591 removed outlier: 3.799A pdb=" N VAL A 577 " --> pdb=" O ALA A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 637 removed outlier: 3.958A pdb=" N PHE A 615 " --> pdb=" O PHE A 611 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG A 616 " --> pdb=" O LYS A 612 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N TYR A 621 " --> pdb=" O PHE A 617 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LEU A 635 " --> pdb=" O ALA A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 662 through 679 Processing helix chain 'A' and resid 684 through 688 Processing helix chain 'A' and resid 691 through 724 removed outlier: 3.721A pdb=" N PHE A 695 " --> pdb=" O TYR A 691 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LEU A 717 " --> pdb=" O MET A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 748 removed outlier: 3.506A pdb=" N PHE A 748 " --> pdb=" O ILE A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 756 Processing helix chain 'B' and resid 150 through 161 removed outlier: 3.651A pdb=" N ASP B 156 " --> pdb=" O PRO B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 167 No H-bonds generated for 'chain 'B' and resid 165 through 167' Processing helix chain 'B' and resid 168 through 177 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 193 through 199 removed outlier: 3.589A pdb=" N LYS B 197 " --> pdb=" O THR B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 221 removed outlier: 3.973A pdb=" N VAL B 212 " --> pdb=" O ASP B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 228 Processing helix chain 'B' and resid 240 through 248 removed outlier: 3.912A pdb=" N ILE B 244 " --> pdb=" O THR B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 297 through 306 Processing helix chain 'B' and resid 323 through 331 Processing helix chain 'B' and resid 335 through 357 removed outlier: 4.264A pdb=" N PHE B 341 " --> pdb=" O GLU B 337 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LYS B 344 " --> pdb=" O LYS B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 365 removed outlier: 3.951A pdb=" N VAL B 365 " --> pdb=" O LEU B 362 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 382 through 391 Processing helix chain 'B' and resid 399 through 403 removed outlier: 3.850A pdb=" N LEU B 402 " --> pdb=" O THR B 399 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER B 403 " --> pdb=" O ARG B 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 399 through 403' Processing helix chain 'B' and resid 432 through 439 Processing helix chain 'B' and resid 445 through 451 Processing helix chain 'B' and resid 452 through 466 Processing helix chain 'B' and resid 466 through 492 Processing helix chain 'B' and resid 504 through 532 Processing helix chain 'B' and resid 549 through 570 Processing helix chain 'B' and resid 573 through 589 Processing helix chain 'B' and resid 590 through 594 Processing helix chain 'B' and resid 596 through 605 removed outlier: 4.588A pdb=" N THR B 601 " --> pdb=" O LYS B 597 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N TYR B 602 " --> pdb=" O LEU B 598 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N MET B 605 " --> pdb=" O THR B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 634 removed outlier: 3.953A pdb=" N PHE B 611 " --> pdb=" O GLN B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 664 through 679 removed outlier: 3.722A pdb=" N THR B 668 " --> pdb=" O GLU B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 689 removed outlier: 4.045A pdb=" N SER B 688 " --> pdb=" O GLU B 684 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N THR B 689 " --> pdb=" O MET B 685 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 684 through 689' Processing helix chain 'B' and resid 691 through 723 Processing helix chain 'B' and resid 725 through 747 removed outlier: 4.819A pdb=" N TRP B 733 " --> pdb=" O SER B 729 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYS B 734 " --> pdb=" O LYS B 730 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU B 735 " --> pdb=" O HIS B 731 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 756 Processing helix chain 'E' and resid 17 through 28 Processing helix chain 'E' and resid 65 through 70 Processing helix chain 'E' and resid 88 through 98 removed outlier: 4.261A pdb=" N LEU E 92 " --> pdb=" O SER E 88 " (cutoff:3.500A) Proline residue: E 96 - end of helix Processing helix chain 'E' and resid 98 through 107 Processing helix chain 'E' and resid 118 through 123 removed outlier: 3.642A pdb=" N ASN E 123 " --> pdb=" O ASP E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 134 Processing helix chain 'E' and resid 140 through 152 Processing helix chain 'E' and resid 168 through 180 removed outlier: 3.537A pdb=" N GLN E 180 " --> pdb=" O ARG E 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 17 through 28 Processing helix chain 'F' and resid 65 through 70 Processing helix chain 'F' and resid 88 through 98 removed outlier: 4.261A pdb=" N LEU F 92 " --> pdb=" O SER F 88 " (cutoff:3.500A) Proline residue: F 96 - end of helix Processing helix chain 'F' and resid 98 through 107 Processing helix chain 'F' and resid 118 through 123 removed outlier: 3.642A pdb=" N ASN F 123 " --> pdb=" O ASP F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 134 Processing helix chain 'F' and resid 140 through 152 Processing helix chain 'F' and resid 168 through 180 removed outlier: 3.537A pdb=" N GLN F 180 " --> pdb=" O ARG F 176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 405 through 409 removed outlier: 6.846A pdb=" N LYS C 405 " --> pdb=" O ASP C 420 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ASP C 420 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LYS C 407 " --> pdb=" O LEU C 418 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU C 418 " --> pdb=" O LYS C 407 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG C 775 " --> pdb=" O VAL C 762 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C 762 " --> pdb=" O ARG C 775 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 405 through 411 removed outlier: 6.842A pdb=" N LYS D 405 " --> pdb=" O ASP D 420 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASP D 420 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LYS D 407 " --> pdb=" O LEU D 418 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU D 418 " --> pdb=" O LYS D 407 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP D 409 " --> pdb=" O SER D 416 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY D 765 " --> pdb=" O ASP D 773 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ARG D 775 " --> pdb=" O THR D 763 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N THR D 763 " --> pdb=" O ARG D 775 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N CYS D 777 " --> pdb=" O MET D 761 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N MET D 761 " --> pdb=" O CYS D 777 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 405 through 409 removed outlier: 6.846A pdb=" N LYS A 405 " --> pdb=" O ASP A 420 " (cutoff:3.500A) removed outlier: 7.359A pdb=" N ASP A 420 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LYS A 407 " --> pdb=" O LEU A 418 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU A 418 " --> pdb=" O LYS A 407 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG A 775 " --> pdb=" O VAL A 762 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL A 762 " --> pdb=" O ARG A 775 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 405 through 411 removed outlier: 6.842A pdb=" N LYS B 405 " --> pdb=" O ASP B 420 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ASP B 420 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LYS B 407 " --> pdb=" O LEU B 418 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU B 418 " --> pdb=" O LYS B 407 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TRP B 409 " --> pdb=" O SER B 416 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY B 765 " --> pdb=" O ASP B 773 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N ARG B 775 " --> pdb=" O THR B 763 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N THR B 763 " --> pdb=" O ARG B 775 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N CYS B 777 " --> pdb=" O MET B 761 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N MET B 761 " --> pdb=" O CYS B 777 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 42 through 48 removed outlier: 4.305A pdb=" N TYR E 42 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE E 4 " --> pdb=" O GLU E 54 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA E 56 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS E 6 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TRP E 58 " --> pdb=" O LYS E 6 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU E 8 " --> pdb=" O TRP E 58 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N VAL E 79 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS E 7 " --> pdb=" O VAL E 79 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU E 81 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL E 9 " --> pdb=" O LEU E 81 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N CYS E 83 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N VAL E 11 " --> pdb=" O CYS E 83 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N SER E 85 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE E 80 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL E 115 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N MET E 82 " --> pdb=" O VAL E 115 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ASN E 117 " --> pdb=" O MET E 82 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE E 84 " --> pdb=" O ASN E 117 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY E 155 " --> pdb=" O ILE E 112 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET E 157 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 42 through 48 removed outlier: 4.305A pdb=" N TYR F 42 " --> pdb=" O LEU F 57 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE F 4 " --> pdb=" O GLU F 54 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N ALA F 56 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS F 6 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N TRP F 58 " --> pdb=" O LYS F 6 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU F 8 " --> pdb=" O TRP F 58 " (cutoff:3.500A) removed outlier: 9.014A pdb=" N VAL F 79 " --> pdb=" O ARG F 5 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N LYS F 7 " --> pdb=" O VAL F 79 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N LEU F 81 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL F 9 " --> pdb=" O LEU F 81 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N CYS F 83 " --> pdb=" O VAL F 9 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N VAL F 11 " --> pdb=" O CYS F 83 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N SER F 85 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ILE F 80 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N VAL F 115 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N MET F 82 " --> pdb=" O VAL F 115 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ASN F 117 " --> pdb=" O MET F 82 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N PHE F 84 " --> pdb=" O ASN F 117 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLY F 155 " --> pdb=" O ILE F 112 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N MET F 157 " --> pdb=" O LEU F 114 " (cutoff:3.500A) 1243 hydrogen bonds defined for protein. 3621 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 2.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3520 1.31 - 1.44: 6176 1.44 - 1.56: 12866 1.56 - 1.69: 10 1.69 - 1.82: 190 Bond restraints: 22762 Sorted by residual: bond pdb=" C PRO E 89 " pdb=" O PRO E 89 " ideal model delta sigma weight residual 1.235 1.184 0.051 1.30e-02 5.92e+03 1.56e+01 bond pdb=" C PRO F 89 " pdb=" O PRO F 89 " ideal model delta sigma weight residual 1.235 1.184 0.051 1.30e-02 5.92e+03 1.56e+01 bond pdb=" N ILE F 46 " pdb=" CA ILE F 46 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.14e-02 7.69e+03 1.00e+01 bond pdb=" N ILE E 46 " pdb=" CA ILE E 46 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.14e-02 7.69e+03 1.00e+01 bond pdb=" C THR B 497 " pdb=" N PRO B 498 " ideal model delta sigma weight residual 1.329 1.366 -0.037 1.18e-02 7.18e+03 9.69e+00 ... (remaining 22757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 29274 2.01 - 4.01: 1420 4.01 - 6.02: 148 6.02 - 8.03: 12 8.03 - 10.03: 10 Bond angle restraints: 30864 Sorted by residual: angle pdb=" N LEU C 180 " pdb=" CA LEU C 180 " pdb=" C LEU C 180 " ideal model delta sigma weight residual 111.71 107.26 4.45 1.15e+00 7.56e-01 1.50e+01 angle pdb=" N LEU A 180 " pdb=" CA LEU A 180 " pdb=" C LEU A 180 " ideal model delta sigma weight residual 111.71 107.26 4.45 1.15e+00 7.56e-01 1.50e+01 angle pdb=" N LYS C 177 " pdb=" CA LYS C 177 " pdb=" C LYS C 177 " ideal model delta sigma weight residual 112.47 107.71 4.76 1.24e+00 6.50e-01 1.47e+01 angle pdb=" N LYS A 177 " pdb=" CA LYS A 177 " pdb=" C LYS A 177 " ideal model delta sigma weight residual 112.47 107.71 4.76 1.24e+00 6.50e-01 1.47e+01 angle pdb=" CA ASP B 182 " pdb=" C ASP B 182 " pdb=" O ASP B 182 " ideal model delta sigma weight residual 121.81 117.36 4.45 1.18e+00 7.18e-01 1.42e+01 ... (remaining 30859 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.10: 13235 31.10 - 62.19: 355 62.19 - 93.29: 22 93.29 - 124.38: 6 124.38 - 155.48: 8 Dihedral angle restraints: 13626 sinusoidal: 5508 harmonic: 8118 Sorted by residual: dihedral pdb=" O2B GDP E 201 " pdb=" O3A GDP E 201 " pdb=" PB GDP E 201 " pdb=" PA GDP E 201 " ideal model delta sinusoidal sigma weight residual -180.00 -65.57 -114.43 1 2.00e+01 2.50e-03 3.39e+01 dihedral pdb=" O2B GDP F 201 " pdb=" O3A GDP F 201 " pdb=" PB GDP F 201 " pdb=" PA GDP F 201 " ideal model delta sinusoidal sigma weight residual -180.00 -65.57 -114.43 1 2.00e+01 2.50e-03 3.39e+01 dihedral pdb=" C5' GDP F 201 " pdb=" O5' GDP F 201 " pdb=" PA GDP F 201 " pdb=" O3A GDP F 201 " ideal model delta sinusoidal sigma weight residual 179.98 -69.30 -110.72 1 2.00e+01 2.50e-03 3.25e+01 ... (remaining 13623 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2959 0.069 - 0.138: 473 0.138 - 0.208: 80 0.208 - 0.277: 20 0.277 - 0.346: 4 Chirality restraints: 3536 Sorted by residual: chirality pdb=" C2 P5S C 801 " pdb=" C1 P5S C 801 " pdb=" C3 P5S C 801 " pdb=" O37 P5S C 801 " both_signs ideal model delta sigma weight residual False 2.59 2.25 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C2 P5S A 801 " pdb=" C1 P5S A 801 " pdb=" C3 P5S A 801 " pdb=" O37 P5S A 801 " both_signs ideal model delta sigma weight residual False 2.59 2.25 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" CA GLU E 64 " pdb=" N GLU E 64 " pdb=" C GLU E 64 " pdb=" CB GLU E 64 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 3533 not shown) Planarity restraints: 3854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN B 307 " -0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO B 308 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO B 308 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 308 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 307 " 0.039 5.00e-02 4.00e+02 5.93e-02 5.62e+00 pdb=" N PRO D 308 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO D 308 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 308 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 577 " 0.011 2.00e-02 2.50e+03 2.19e-02 4.82e+00 pdb=" C VAL D 577 " -0.038 2.00e-02 2.50e+03 pdb=" O VAL D 577 " 0.014 2.00e-02 2.50e+03 pdb=" N MET D 578 " 0.013 2.00e-02 2.50e+03 ... (remaining 3851 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 178 2.62 - 3.19: 20311 3.19 - 3.76: 35394 3.76 - 4.33: 48025 4.33 - 4.90: 78381 Nonbonded interactions: 182289 Sorted by model distance: nonbonded pdb=" O THR F 37 " pdb="MG MG F 202 " model vdw 2.050 2.170 nonbonded pdb=" O THR E 37 " pdb="MG MG E 202 " model vdw 2.050 2.170 nonbonded pdb=" O1B GDP F 201 " pdb="MG MG F 202 " model vdw 2.074 2.170 nonbonded pdb=" O1B GDP E 201 " pdb="MG MG E 202 " model vdw 2.074 2.170 nonbonded pdb=" OG SER C 767 " pdb=" OD1 ASP C 769 " model vdw 2.205 3.040 ... (remaining 182284 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: 0.04 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' } ncs_group { reference = chain 'D' selection = chain 'B' } ncs_group { reference = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 21.580 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 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 : 0.006 0.053 22766 Z= 0.400 Angle : 0.891 10.035 30872 Z= 0.587 Chirality : 0.056 0.346 3536 Planarity : 0.005 0.059 3854 Dihedral : 14.858 155.477 8374 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.04 % Favored : 97.88 % Rotamer: Outliers : 0.67 % Allowed : 1.66 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.16), residues: 2742 helix: 1.02 (0.13), residues: 1654 sheet: -0.67 (0.43), residues: 156 loop : -0.31 (0.20), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 271 TYR 0.014 0.001 TYR D 591 PHE 0.024 0.002 PHE B 695 TRP 0.023 0.002 TRP A 785 HIS 0.003 0.001 HIS B 252 Details of bonding type rmsd covalent geometry : bond 0.00573 (22762) covalent geometry : angle 0.89065 (30864) SS BOND : bond 0.00332 ( 4) SS BOND : angle 0.26687 ( 8) hydrogen bonds : bond 0.15205 ( 1243) hydrogen bonds : angle 6.07090 ( 3621) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 488 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 461 ASP cc_start: 0.8427 (t70) cc_final: 0.8181 (t0) REVERT: C 605 MET cc_start: 0.5093 (ttt) cc_final: 0.4821 (ttt) REVERT: C 685 MET cc_start: 0.8059 (mpp) cc_final: 0.7790 (mpp) REVERT: C 686 LEU cc_start: 0.8418 (pp) cc_final: 0.8053 (mt) REVERT: D 215 ASP cc_start: 0.7745 (t0) cc_final: 0.7476 (t0) REVERT: D 331 ILE cc_start: 0.8557 (tp) cc_final: 0.8306 (tp) REVERT: D 495 GLU cc_start: 0.6051 (OUTLIER) cc_final: 0.5737 (pm20) REVERT: D 500 TYR cc_start: 0.6081 (m-80) cc_final: 0.4451 (m-10) REVERT: A 461 ASP cc_start: 0.8430 (t70) cc_final: 0.8182 (t0) REVERT: A 605 MET cc_start: 0.5094 (ttt) cc_final: 0.4821 (ttt) REVERT: A 685 MET cc_start: 0.8059 (mpp) cc_final: 0.7791 (mpp) REVERT: A 686 LEU cc_start: 0.8419 (pp) cc_final: 0.8053 (mt) REVERT: B 215 ASP cc_start: 0.7744 (t0) cc_final: 0.7475 (t0) REVERT: B 331 ILE cc_start: 0.8558 (tp) cc_final: 0.8306 (tp) REVERT: B 495 GLU cc_start: 0.6050 (OUTLIER) cc_final: 0.5736 (pm20) REVERT: B 500 TYR cc_start: 0.6080 (m-80) cc_final: 0.4451 (m-10) outliers start: 16 outliers final: 0 residues processed: 504 average time/residue: 0.1464 time to fit residues: 115.5806 Evaluate side-chains 385 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 383 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 495 GLU Chi-restraints excluded: chain B residue 495 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 0.0020 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 8.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.6980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 GLN ** C 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 307 ASN D 201 ASN D 322 ASN D 338 ASN D 607 GLN A 260 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 307 ASN B 201 ASN B 322 ASN B 338 ASN B 607 GLN E 94 ASN F 94 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.194973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.146180 restraints weight = 33947.770| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 2.58 r_work: 0.3634 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22766 Z= 0.135 Angle : 0.595 12.111 30872 Z= 0.299 Chirality : 0.040 0.160 3536 Planarity : 0.004 0.049 3854 Dihedral : 10.369 160.340 3156 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.54 % Allowed : 10.14 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.16), residues: 2742 helix: 1.29 (0.13), residues: 1672 sheet: -0.67 (0.40), residues: 170 loop : -0.31 (0.21), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 271 TYR 0.014 0.001 TYR A 253 PHE 0.022 0.002 PHE C 617 TRP 0.015 0.001 TRP A 737 HIS 0.003 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00306 (22762) covalent geometry : angle 0.59520 (30864) SS BOND : bond 0.00150 ( 4) SS BOND : angle 0.28382 ( 8) hydrogen bonds : bond 0.03876 ( 1243) hydrogen bonds : angle 4.58303 ( 3621) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 422 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 461 ASP cc_start: 0.8954 (t70) cc_final: 0.8749 (t0) REVERT: C 511 LEU cc_start: 0.7589 (tp) cc_final: 0.7242 (tp) REVERT: C 686 LEU cc_start: 0.8266 (pp) cc_final: 0.7898 (mt) REVERT: D 225 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7852 (pt0) REVERT: D 331 ILE cc_start: 0.9085 (tp) cc_final: 0.8721 (tp) REVERT: D 685 MET cc_start: 0.8525 (mtp) cc_final: 0.8295 (mtp) REVERT: A 461 ASP cc_start: 0.8961 (t70) cc_final: 0.8753 (t0) REVERT: A 511 LEU cc_start: 0.7591 (tp) cc_final: 0.7242 (tp) REVERT: A 678 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8568 (mm) REVERT: A 686 LEU cc_start: 0.8280 (pp) cc_final: 0.7893 (mt) REVERT: B 225 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7852 (pt0) REVERT: B 331 ILE cc_start: 0.9089 (tp) cc_final: 0.8724 (tp) REVERT: B 685 MET cc_start: 0.8525 (mtp) cc_final: 0.8299 (mtp) REVERT: E 40 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7392 (mt-10) REVERT: E 104 LYS cc_start: 0.8218 (tptt) cc_final: 0.7731 (mmmt) REVERT: E 172 GLU cc_start: 0.6767 (tm-30) cc_final: 0.6552 (tm-30) REVERT: F 40 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7388 (mt-10) REVERT: F 104 LYS cc_start: 0.8215 (tptt) cc_final: 0.7727 (mmmt) REVERT: F 172 GLU cc_start: 0.6764 (tm-30) cc_final: 0.6553 (tm-30) outliers start: 37 outliers final: 21 residues processed: 439 average time/residue: 0.1357 time to fit residues: 96.1875 Evaluate side-chains 394 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 372 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 337 GLU Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 741 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 691 TYR Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 337 GLU Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 97 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 248 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 0.0070 chunk 27 optimal weight: 3.9990 chunk 216 optimal weight: 10.0000 chunk 93 optimal weight: 0.7980 chunk 204 optimal weight: 3.9990 chunk 226 optimal weight: 0.7980 chunk 142 optimal weight: 0.6980 chunk 271 optimal weight: 30.0000 overall best weight: 1.0600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 222 ASN ** C 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 297 GLN C 322 ASN A 222 ASN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 297 GLN A 322 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.199228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.149252 restraints weight = 33731.276| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.62 r_work: 0.3581 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 22766 Z= 0.149 Angle : 0.581 12.523 30872 Z= 0.289 Chirality : 0.040 0.182 3536 Planarity : 0.004 0.045 3854 Dihedral : 9.833 160.987 3150 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.41 % Allowed : 12.43 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.16), residues: 2742 helix: 1.38 (0.12), residues: 1674 sheet: -0.37 (0.43), residues: 156 loop : -0.52 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 271 TYR 0.014 0.001 TYR D 500 PHE 0.023 0.002 PHE A 669 TRP 0.014 0.001 TRP A 737 HIS 0.004 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00350 (22762) covalent geometry : angle 0.58133 (30864) SS BOND : bond 0.00149 ( 4) SS BOND : angle 0.19324 ( 8) hydrogen bonds : bond 0.03597 ( 1243) hydrogen bonds : angle 4.37555 ( 3621) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 403 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 457 GLU cc_start: 0.8398 (mm-30) cc_final: 0.7968 (mp0) REVERT: C 461 ASP cc_start: 0.9004 (t70) cc_final: 0.8742 (t0) REVERT: C 511 LEU cc_start: 0.7584 (tp) cc_final: 0.7246 (tp) REVERT: C 678 ILE cc_start: 0.8801 (OUTLIER) cc_final: 0.8543 (mm) REVERT: C 686 LEU cc_start: 0.8215 (pp) cc_final: 0.7929 (mt) REVERT: D 223 MET cc_start: 0.7757 (tpp) cc_final: 0.7509 (tpp) REVERT: D 225 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7891 (pt0) REVERT: D 331 ILE cc_start: 0.9192 (tp) cc_final: 0.8828 (tp) REVERT: D 685 MET cc_start: 0.8660 (mtp) cc_final: 0.8453 (mtp) REVERT: A 457 GLU cc_start: 0.8403 (mm-30) cc_final: 0.7968 (mp0) REVERT: A 461 ASP cc_start: 0.9010 (t70) cc_final: 0.8744 (t0) REVERT: A 511 LEU cc_start: 0.7600 (tp) cc_final: 0.7260 (tp) REVERT: A 678 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8530 (mm) REVERT: A 686 LEU cc_start: 0.8227 (pp) cc_final: 0.7961 (mt) REVERT: B 223 MET cc_start: 0.7753 (tpp) cc_final: 0.7506 (tpp) REVERT: B 225 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7884 (pt0) REVERT: B 331 ILE cc_start: 0.9193 (tp) cc_final: 0.8828 (tp) REVERT: B 685 MET cc_start: 0.8650 (mtp) cc_final: 0.8445 (mtp) REVERT: E 172 GLU cc_start: 0.6654 (tm-30) cc_final: 0.6415 (tm-30) REVERT: F 172 GLU cc_start: 0.6656 (tm-30) cc_final: 0.6420 (tm-30) outliers start: 58 outliers final: 30 residues processed: 427 average time/residue: 0.1340 time to fit residues: 93.6980 Evaluate side-chains 381 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 349 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 624 PHE Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 628 TYR Chi-restraints excluded: chain D residue 741 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 691 TYR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 97 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 213 optimal weight: 0.7980 chunk 127 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 197 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 103 optimal weight: 9.9990 chunk 118 optimal weight: 1.9990 chunk 274 optimal weight: 5.9990 chunk 173 optimal weight: 6.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 GLN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.199531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.148023 restraints weight = 33908.621| |-----------------------------------------------------------------------------| r_work (start): 0.3793 rms_B_bonded: 2.49 r_work: 0.3591 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22766 Z= 0.129 Angle : 0.586 13.475 30872 Z= 0.286 Chirality : 0.039 0.159 3536 Planarity : 0.004 0.042 3854 Dihedral : 9.479 158.983 3150 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.45 % Allowed : 14.09 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.16), residues: 2742 helix: 1.50 (0.13), residues: 1684 sheet: -0.38 (0.41), residues: 152 loop : -0.57 (0.20), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 271 TYR 0.016 0.001 TYR D 500 PHE 0.015 0.001 PHE A 617 TRP 0.014 0.001 TRP A 785 HIS 0.003 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00299 (22762) covalent geometry : angle 0.58639 (30864) SS BOND : bond 0.00118 ( 4) SS BOND : angle 0.17334 ( 8) hydrogen bonds : bond 0.03345 ( 1243) hydrogen bonds : angle 4.26893 ( 3621) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 362 time to evaluate : 0.881 Fit side-chains REVERT: C 225 GLU cc_start: 0.6426 (tp30) cc_final: 0.6174 (tp30) REVERT: C 457 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7949 (mp0) REVERT: C 511 LEU cc_start: 0.7606 (tp) cc_final: 0.7245 (tp) REVERT: C 678 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8512 (mm) REVERT: D 223 MET cc_start: 0.7872 (tpp) cc_final: 0.7484 (tpp) REVERT: D 225 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8001 (pt0) REVERT: D 331 ILE cc_start: 0.9181 (tp) cc_final: 0.8846 (tp) REVERT: D 449 MET cc_start: 0.8690 (mtt) cc_final: 0.8420 (mtt) REVERT: D 525 PHE cc_start: 0.7761 (OUTLIER) cc_final: 0.7050 (m-80) REVERT: A 225 GLU cc_start: 0.6441 (tp30) cc_final: 0.6193 (tp30) REVERT: A 457 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7946 (mp0) REVERT: A 511 LEU cc_start: 0.7613 (tp) cc_final: 0.7264 (tp) REVERT: A 678 ILE cc_start: 0.8742 (OUTLIER) cc_final: 0.8514 (mm) REVERT: B 223 MET cc_start: 0.7866 (tpp) cc_final: 0.7478 (tpp) REVERT: B 225 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7996 (pt0) REVERT: B 331 ILE cc_start: 0.9182 (tp) cc_final: 0.8848 (tp) REVERT: B 449 MET cc_start: 0.8690 (mtt) cc_final: 0.8424 (mtt) REVERT: E 16 CYS cc_start: 0.6139 (m) cc_final: 0.5383 (t) REVERT: E 40 GLU cc_start: 0.8087 (mt-10) cc_final: 0.7289 (mt-10) REVERT: E 78 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7749 (t0) REVERT: E 172 GLU cc_start: 0.6595 (tm-30) cc_final: 0.6387 (tm-30) REVERT: F 16 CYS cc_start: 0.6138 (m) cc_final: 0.5394 (t) REVERT: F 40 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7284 (mt-10) REVERT: F 78 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7911 (t0) REVERT: F 172 GLU cc_start: 0.6599 (tm-30) cc_final: 0.6376 (tm-30) outliers start: 59 outliers final: 32 residues processed: 394 average time/residue: 0.1311 time to fit residues: 84.8819 Evaluate side-chains 377 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 340 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 624 PHE Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 782 GLU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 525 PHE Chi-restraints excluded: chain D residue 628 TYR Chi-restraints excluded: chain D residue 741 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 691 TYR Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 45 ASP Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 45 ASP Chi-restraints excluded: chain F residue 78 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 10 optimal weight: 0.6980 chunk 220 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 155 optimal weight: 30.0000 chunk 193 optimal weight: 0.0370 chunk 118 optimal weight: 0.9980 chunk 136 optimal weight: 0.0870 chunk 210 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 59 optimal weight: 5.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.195307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.146395 restraints weight = 33965.805| |-----------------------------------------------------------------------------| r_work (start): 0.3868 rms_B_bonded: 2.40 r_work: 0.3643 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22766 Z= 0.112 Angle : 0.567 14.283 30872 Z= 0.275 Chirality : 0.039 0.199 3536 Planarity : 0.004 0.039 3854 Dihedral : 9.160 155.601 3150 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.45 % Allowed : 14.51 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.16), residues: 2742 helix: 1.65 (0.13), residues: 1670 sheet: -0.28 (0.41), residues: 152 loop : -0.48 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 271 TYR 0.017 0.001 TYR D 500 PHE 0.027 0.001 PHE C 592 TRP 0.019 0.001 TRP C 785 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00254 (22762) covalent geometry : angle 0.56682 (30864) SS BOND : bond 0.00057 ( 4) SS BOND : angle 0.17903 ( 8) hydrogen bonds : bond 0.03164 ( 1243) hydrogen bonds : angle 4.16157 ( 3621) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 357 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 225 GLU cc_start: 0.6413 (tp30) cc_final: 0.6140 (tp30) REVERT: C 457 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8004 (mp0) REVERT: C 511 LEU cc_start: 0.7555 (tp) cc_final: 0.7210 (tp) REVERT: C 678 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8488 (mm) REVERT: C 703 ILE cc_start: 0.8916 (mt) cc_final: 0.8669 (pt) REVERT: D 223 MET cc_start: 0.7889 (tpp) cc_final: 0.7563 (tpp) REVERT: D 225 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7988 (pt0) REVERT: D 331 ILE cc_start: 0.9151 (tp) cc_final: 0.8819 (tp) REVERT: D 449 MET cc_start: 0.8677 (mtt) cc_final: 0.8388 (mtt) REVERT: D 525 PHE cc_start: 0.7786 (OUTLIER) cc_final: 0.7019 (m-80) REVERT: A 225 GLU cc_start: 0.6422 (tp30) cc_final: 0.6150 (tp30) REVERT: A 457 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7996 (mp0) REVERT: A 511 LEU cc_start: 0.7563 (tp) cc_final: 0.7215 (tp) REVERT: A 678 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8495 (mm) REVERT: A 703 ILE cc_start: 0.8914 (mt) cc_final: 0.8665 (pt) REVERT: B 223 MET cc_start: 0.7884 (tpp) cc_final: 0.7561 (tpp) REVERT: B 225 GLU cc_start: 0.8318 (mt-10) cc_final: 0.7991 (pt0) REVERT: B 331 ILE cc_start: 0.9155 (tp) cc_final: 0.8822 (tp) REVERT: B 449 MET cc_start: 0.8680 (mtt) cc_final: 0.8398 (mtt) REVERT: B 525 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.7099 (m-80) REVERT: E 16 CYS cc_start: 0.6246 (m) cc_final: 0.5458 (t) REVERT: E 40 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7507 (mt-10) REVERT: E 104 LYS cc_start: 0.8337 (tptt) cc_final: 0.7895 (mmmt) REVERT: E 172 GLU cc_start: 0.6566 (tm-30) cc_final: 0.6349 (tm-30) REVERT: F 16 CYS cc_start: 0.6247 (m) cc_final: 0.5429 (t) REVERT: F 40 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7510 (mt-10) REVERT: F 104 LYS cc_start: 0.8330 (tptt) cc_final: 0.7885 (mmmt) REVERT: F 172 GLU cc_start: 0.6568 (tm-30) cc_final: 0.6365 (tm-30) outliers start: 59 outliers final: 40 residues processed: 390 average time/residue: 0.1309 time to fit residues: 84.3186 Evaluate side-chains 389 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 345 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 624 PHE Chi-restraints excluded: chain C residue 678 ILE Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 732 ILE Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 782 GLU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 525 PHE Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 628 TYR Chi-restraints excluded: chain D residue 741 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 678 ILE Chi-restraints excluded: chain A residue 691 TYR Chi-restraints excluded: chain A residue 732 ILE Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 97 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 236 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.194691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.144728 restraints weight = 34045.276| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.41 r_work: 0.3624 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22766 Z= 0.117 Angle : 0.561 15.079 30872 Z= 0.272 Chirality : 0.039 0.170 3536 Planarity : 0.004 0.045 3854 Dihedral : 8.998 151.330 3150 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.24 % Allowed : 15.46 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.16), residues: 2742 helix: 1.71 (0.13), residues: 1668 sheet: -0.30 (0.42), residues: 152 loop : -0.48 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 271 TYR 0.017 0.001 TYR D 500 PHE 0.017 0.001 PHE D 674 TRP 0.019 0.001 TRP C 785 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00270 (22762) covalent geometry : angle 0.56130 (30864) SS BOND : bond 0.00089 ( 4) SS BOND : angle 0.15980 ( 8) hydrogen bonds : bond 0.03135 ( 1243) hydrogen bonds : angle 4.12504 ( 3621) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 360 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 225 GLU cc_start: 0.6610 (tp30) cc_final: 0.6266 (tp30) REVERT: C 457 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8004 (mp0) REVERT: C 511 LEU cc_start: 0.7565 (tp) cc_final: 0.7224 (tp) REVERT: C 703 ILE cc_start: 0.8916 (mt) cc_final: 0.8665 (pt) REVERT: D 223 MET cc_start: 0.7877 (tpp) cc_final: 0.7548 (tpp) REVERT: D 225 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8036 (pt0) REVERT: D 331 ILE cc_start: 0.9157 (tp) cc_final: 0.8840 (tp) REVERT: D 387 GLN cc_start: 0.8370 (mt0) cc_final: 0.8098 (mt0) REVERT: D 449 MET cc_start: 0.8694 (mtt) cc_final: 0.8419 (mtt) REVERT: D 525 PHE cc_start: 0.7851 (OUTLIER) cc_final: 0.7029 (m-80) REVERT: A 225 GLU cc_start: 0.6511 (tp30) cc_final: 0.6186 (tp30) REVERT: A 457 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8009 (mp0) REVERT: A 511 LEU cc_start: 0.7569 (tp) cc_final: 0.7226 (tp) REVERT: A 703 ILE cc_start: 0.8913 (mt) cc_final: 0.8661 (pt) REVERT: B 223 MET cc_start: 0.7875 (tpp) cc_final: 0.7546 (tpp) REVERT: B 225 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8035 (pt0) REVERT: B 331 ILE cc_start: 0.9158 (tp) cc_final: 0.8840 (tp) REVERT: B 387 GLN cc_start: 0.8367 (mt0) cc_final: 0.8093 (mt0) REVERT: B 449 MET cc_start: 0.8663 (mtt) cc_final: 0.8393 (mtt) REVERT: B 525 PHE cc_start: 0.7876 (OUTLIER) cc_final: 0.7097 (m-80) REVERT: B 696 ILE cc_start: 0.8340 (mt) cc_final: 0.8109 (mm) REVERT: E 16 CYS cc_start: 0.6231 (m) cc_final: 0.5542 (t) REVERT: E 40 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7746 (mt-10) REVERT: E 82 MET cc_start: 0.6490 (mtm) cc_final: 0.5386 (pmm) REVERT: E 104 LYS cc_start: 0.8509 (tptt) cc_final: 0.8041 (mmmt) REVERT: F 16 CYS cc_start: 0.6209 (m) cc_final: 0.5541 (t) REVERT: F 40 GLU cc_start: 0.8095 (mt-10) cc_final: 0.7745 (mt-10) REVERT: F 82 MET cc_start: 0.6489 (mtm) cc_final: 0.5389 (pmm) REVERT: F 104 LYS cc_start: 0.8520 (tptt) cc_final: 0.8048 (mmmt) outliers start: 54 outliers final: 40 residues processed: 386 average time/residue: 0.1290 time to fit residues: 82.5534 Evaluate side-chains 388 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 346 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 624 PHE Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 782 GLU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 525 PHE Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 628 TYR Chi-restraints excluded: chain D residue 741 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 691 TYR Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 97 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 66 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 81 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 151 optimal weight: 0.5980 chunk 235 optimal weight: 0.9980 chunk 182 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 254 optimal weight: 5.9990 chunk 227 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 HIS C 201 ASN A 176 HIS A 201 ASN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 528 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.189475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.135746 restraints weight = 34326.185| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.33 r_work: 0.3558 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22766 Z= 0.124 Angle : 0.570 15.231 30872 Z= 0.277 Chirality : 0.039 0.185 3536 Planarity : 0.004 0.047 3854 Dihedral : 8.473 145.751 3150 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.54 % Allowed : 15.75 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.16), residues: 2742 helix: 1.70 (0.13), residues: 1668 sheet: -0.30 (0.42), residues: 152 loop : -0.48 (0.20), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 271 TYR 0.018 0.001 TYR B 500 PHE 0.018 0.001 PHE B 669 TRP 0.023 0.001 TRP C 785 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00288 (22762) covalent geometry : angle 0.57041 (30864) SS BOND : bond 0.00098 ( 4) SS BOND : angle 0.15791 ( 8) hydrogen bonds : bond 0.03157 ( 1243) hydrogen bonds : angle 4.12348 ( 3621) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 369 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 225 GLU cc_start: 0.6557 (tp30) cc_final: 0.6217 (tp30) REVERT: C 457 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7979 (mp0) REVERT: C 511 LEU cc_start: 0.7543 (tp) cc_final: 0.7219 (tp) REVERT: C 703 ILE cc_start: 0.8894 (mt) cc_final: 0.8634 (pt) REVERT: C 709 LEU cc_start: 0.8410 (tt) cc_final: 0.8109 (tp) REVERT: C 718 MET cc_start: 0.4983 (mtp) cc_final: 0.4740 (mtp) REVERT: D 223 MET cc_start: 0.7938 (tpp) cc_final: 0.7596 (tpp) REVERT: D 225 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8010 (pt0) REVERT: D 331 ILE cc_start: 0.9162 (tp) cc_final: 0.8847 (tp) REVERT: D 387 GLN cc_start: 0.8378 (mt0) cc_final: 0.8080 (mt0) REVERT: D 400 ARG cc_start: 0.8198 (ptm-80) cc_final: 0.7944 (ttp80) REVERT: D 449 MET cc_start: 0.8669 (mtt) cc_final: 0.8379 (mtt) REVERT: D 525 PHE cc_start: 0.7862 (OUTLIER) cc_final: 0.7018 (m-80) REVERT: D 563 SER cc_start: 0.7983 (p) cc_final: 0.7712 (p) REVERT: D 605 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.5401 (ptt) REVERT: A 225 GLU cc_start: 0.6697 (tp30) cc_final: 0.6330 (tp30) REVERT: A 457 GLU cc_start: 0.8402 (mm-30) cc_final: 0.7984 (mp0) REVERT: A 511 LEU cc_start: 0.7544 (tp) cc_final: 0.7219 (tp) REVERT: A 703 ILE cc_start: 0.8889 (mt) cc_final: 0.8635 (pt) REVERT: A 709 LEU cc_start: 0.8401 (tt) cc_final: 0.8099 (tp) REVERT: A 718 MET cc_start: 0.4980 (mtp) cc_final: 0.4738 (mtp) REVERT: B 223 MET cc_start: 0.7931 (tpp) cc_final: 0.7596 (tpp) REVERT: B 225 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8010 (pt0) REVERT: B 331 ILE cc_start: 0.9165 (tp) cc_final: 0.8849 (tp) REVERT: B 387 GLN cc_start: 0.8374 (mt0) cc_final: 0.8074 (mt0) REVERT: B 400 ARG cc_start: 0.8203 (ptm-80) cc_final: 0.7951 (ttp80) REVERT: B 449 MET cc_start: 0.8683 (mtt) cc_final: 0.8355 (mtt) REVERT: B 525 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7060 (m-80) REVERT: B 563 SER cc_start: 0.7985 (p) cc_final: 0.7713 (p) REVERT: B 605 MET cc_start: 0.5782 (OUTLIER) cc_final: 0.5410 (ptt) REVERT: B 674 PHE cc_start: 0.7839 (t80) cc_final: 0.7621 (t80) REVERT: B 696 ILE cc_start: 0.8354 (mt) cc_final: 0.8123 (mm) REVERT: E 16 CYS cc_start: 0.6078 (m) cc_final: 0.5624 (t) REVERT: E 40 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7734 (mt-10) REVERT: E 78 ASP cc_start: 0.8253 (OUTLIER) cc_final: 0.8015 (t0) REVERT: E 82 MET cc_start: 0.6452 (mtm) cc_final: 0.5318 (pmm) REVERT: E 104 LYS cc_start: 0.8486 (tptt) cc_final: 0.8034 (mmmt) REVERT: E 172 GLU cc_start: 0.6532 (tm-30) cc_final: 0.6241 (tm-30) REVERT: E 173 MET cc_start: 0.8371 (tmm) cc_final: 0.8110 (tmm) REVERT: F 16 CYS cc_start: 0.6067 (m) cc_final: 0.5632 (t) REVERT: F 40 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7733 (mt-10) REVERT: F 78 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.8016 (t0) REVERT: F 82 MET cc_start: 0.6492 (mtm) cc_final: 0.5398 (pmm) REVERT: F 104 LYS cc_start: 0.8482 (tptt) cc_final: 0.8031 (mmmt) REVERT: F 172 GLU cc_start: 0.6476 (tm-30) cc_final: 0.6182 (tm-30) REVERT: F 173 MET cc_start: 0.8428 (tmm) cc_final: 0.8144 (tmm) outliers start: 61 outliers final: 40 residues processed: 405 average time/residue: 0.1402 time to fit residues: 92.9959 Evaluate side-chains 400 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 354 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 624 PHE Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 782 GLU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 525 PHE Chi-restraints excluded: chain D residue 605 MET Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 628 TYR Chi-restraints excluded: chain D residue 741 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 691 TYR Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 628 TYR Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain F residue 78 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 165 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 132 optimal weight: 0.0020 chunk 37 optimal weight: 0.6980 chunk 267 optimal weight: 9.9990 chunk 58 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 203 optimal weight: 1.9990 chunk 254 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 21 optimal weight: 0.3980 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 ASN C 309 HIS C 528 ASN A 201 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.189378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.137891 restraints weight = 34308.188| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.73 r_work: 0.3512 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22766 Z= 0.126 Angle : 0.574 15.738 30872 Z= 0.277 Chirality : 0.039 0.189 3536 Planarity : 0.004 0.049 3854 Dihedral : 8.147 139.571 3150 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.62 % Allowed : 16.58 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.16), residues: 2742 helix: 1.69 (0.13), residues: 1680 sheet: -0.30 (0.42), residues: 152 loop : -0.54 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 336 TYR 0.027 0.001 TYR D 500 PHE 0.016 0.001 PHE B 674 TRP 0.018 0.001 TRP C 785 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00294 (22762) covalent geometry : angle 0.57444 (30864) SS BOND : bond 0.00105 ( 4) SS BOND : angle 0.15965 ( 8) hydrogen bonds : bond 0.03164 ( 1243) hydrogen bonds : angle 4.12617 ( 3621) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 347 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 225 GLU cc_start: 0.6594 (tp30) cc_final: 0.6225 (tp30) REVERT: C 457 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8042 (mp0) REVERT: C 511 LEU cc_start: 0.7506 (tp) cc_final: 0.7195 (tp) REVERT: C 528 ASN cc_start: 0.6753 (m-40) cc_final: 0.6496 (m110) REVERT: C 621 TYR cc_start: 0.7156 (OUTLIER) cc_final: 0.6429 (t80) REVERT: C 703 ILE cc_start: 0.8859 (mt) cc_final: 0.8606 (pt) REVERT: D 223 MET cc_start: 0.7947 (tpp) cc_final: 0.7595 (tpp) REVERT: D 225 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8071 (pt0) REVERT: D 331 ILE cc_start: 0.9172 (tp) cc_final: 0.8845 (tp) REVERT: D 387 GLN cc_start: 0.8422 (mt0) cc_final: 0.8093 (mt0) REVERT: D 400 ARG cc_start: 0.8258 (ptm-80) cc_final: 0.8004 (ttp80) REVERT: D 449 MET cc_start: 0.8759 (mtt) cc_final: 0.8435 (mtm) REVERT: D 525 PHE cc_start: 0.7877 (OUTLIER) cc_final: 0.7026 (m-80) REVERT: D 563 SER cc_start: 0.7933 (p) cc_final: 0.7652 (p) REVERT: D 605 MET cc_start: 0.5847 (OUTLIER) cc_final: 0.5457 (ptt) REVERT: D 674 PHE cc_start: 0.7810 (t80) cc_final: 0.7606 (t80) REVERT: A 225 GLU cc_start: 0.6555 (tp30) cc_final: 0.6194 (tp30) REVERT: A 457 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8046 (mp0) REVERT: A 511 LEU cc_start: 0.7508 (tp) cc_final: 0.7195 (tp) REVERT: A 528 ASN cc_start: 0.6695 (m-40) cc_final: 0.6259 (m-40) REVERT: A 621 TYR cc_start: 0.7156 (OUTLIER) cc_final: 0.6429 (t80) REVERT: B 223 MET cc_start: 0.7949 (tpp) cc_final: 0.7600 (tpp) REVERT: B 225 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8076 (pt0) REVERT: B 331 ILE cc_start: 0.9172 (tp) cc_final: 0.8843 (tp) REVERT: B 387 GLN cc_start: 0.8419 (mt0) cc_final: 0.8094 (mt0) REVERT: B 400 ARG cc_start: 0.8256 (ptm-80) cc_final: 0.8006 (ttp80) REVERT: B 525 PHE cc_start: 0.7891 (OUTLIER) cc_final: 0.7087 (m-80) REVERT: B 563 SER cc_start: 0.7956 (p) cc_final: 0.7673 (p) REVERT: B 605 MET cc_start: 0.5844 (OUTLIER) cc_final: 0.5451 (ptt) REVERT: B 674 PHE cc_start: 0.7870 (t80) cc_final: 0.7664 (t80) REVERT: B 696 ILE cc_start: 0.8350 (mt) cc_final: 0.8133 (mm) REVERT: E 16 CYS cc_start: 0.5915 (m) cc_final: 0.5487 (t) REVERT: E 40 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7731 (mt-10) REVERT: E 78 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7948 (t0) REVERT: E 82 MET cc_start: 0.6540 (mtm) cc_final: 0.5392 (pmm) REVERT: E 104 LYS cc_start: 0.8422 (tptt) cc_final: 0.8000 (mmmt) REVERT: E 172 GLU cc_start: 0.6522 (tm-30) cc_final: 0.6175 (tm-30) REVERT: E 173 MET cc_start: 0.8394 (tmm) cc_final: 0.8121 (tmm) REVERT: F 16 CYS cc_start: 0.5892 (m) cc_final: 0.5488 (t) REVERT: F 40 GLU cc_start: 0.8060 (mt-10) cc_final: 0.7732 (mt-10) REVERT: F 78 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7949 (t0) REVERT: F 82 MET cc_start: 0.6590 (mtm) cc_final: 0.5483 (pmm) REVERT: F 104 LYS cc_start: 0.8420 (tptt) cc_final: 0.7997 (mmmt) REVERT: F 173 MET cc_start: 0.8409 (tmm) cc_final: 0.8135 (tmm) outliers start: 63 outliers final: 41 residues processed: 385 average time/residue: 0.1355 time to fit residues: 85.6086 Evaluate side-chains 393 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 344 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 621 TYR Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 624 PHE Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 782 GLU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 525 PHE Chi-restraints excluded: chain D residue 605 MET Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 741 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 691 TYR Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 605 MET Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 78 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 120 optimal weight: 8.9990 chunk 268 optimal weight: 1.9990 chunk 58 optimal weight: 20.0000 chunk 21 optimal weight: 0.9990 chunk 229 optimal weight: 0.7980 chunk 176 optimal weight: 0.6980 chunk 219 optimal weight: 0.7980 chunk 245 optimal weight: 2.9990 chunk 258 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.188834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.136109 restraints weight = 34157.036| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.56 r_work: 0.3507 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22766 Z= 0.129 Angle : 0.587 12.187 30872 Z= 0.284 Chirality : 0.040 0.190 3536 Planarity : 0.004 0.050 3854 Dihedral : 7.995 134.580 3150 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.41 % Allowed : 16.71 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.16), residues: 2742 helix: 1.69 (0.13), residues: 1678 sheet: -0.25 (0.42), residues: 152 loop : -0.52 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 336 TYR 0.017 0.001 TYR B 500 PHE 0.029 0.001 PHE A 669 TRP 0.024 0.001 TRP C 785 HIS 0.004 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00302 (22762) covalent geometry : angle 0.58728 (30864) SS BOND : bond 0.00102 ( 4) SS BOND : angle 0.16002 ( 8) hydrogen bonds : bond 0.03183 ( 1243) hydrogen bonds : angle 4.13399 ( 3621) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 354 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 225 GLU cc_start: 0.6605 (tp30) cc_final: 0.6248 (tp30) REVERT: C 457 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8049 (mp0) REVERT: C 511 LEU cc_start: 0.7596 (tp) cc_final: 0.7292 (tp) REVERT: C 621 TYR cc_start: 0.7178 (OUTLIER) cc_final: 0.6420 (t80) REVERT: C 703 ILE cc_start: 0.8917 (mt) cc_final: 0.8636 (pt) REVERT: D 223 MET cc_start: 0.7950 (tpp) cc_final: 0.7620 (tpp) REVERT: D 225 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8072 (pt0) REVERT: D 387 GLN cc_start: 0.8426 (mt0) cc_final: 0.8109 (mt0) REVERT: D 400 ARG cc_start: 0.8271 (ptm-80) cc_final: 0.8016 (ttp80) REVERT: D 525 PHE cc_start: 0.7970 (OUTLIER) cc_final: 0.7083 (m-80) REVERT: D 563 SER cc_start: 0.7933 (p) cc_final: 0.7665 (p) REVERT: A 225 GLU cc_start: 0.6604 (tp30) cc_final: 0.6249 (tp30) REVERT: A 457 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8057 (mp0) REVERT: A 511 LEU cc_start: 0.7599 (tp) cc_final: 0.7296 (tp) REVERT: A 621 TYR cc_start: 0.7171 (OUTLIER) cc_final: 0.6415 (t80) REVERT: A 703 ILE cc_start: 0.8887 (mt) cc_final: 0.8626 (pt) REVERT: B 223 MET cc_start: 0.7947 (tpp) cc_final: 0.7621 (tpp) REVERT: B 225 GLU cc_start: 0.8435 (mt-10) cc_final: 0.8072 (pt0) REVERT: B 387 GLN cc_start: 0.8422 (mt0) cc_final: 0.8101 (mt0) REVERT: B 400 ARG cc_start: 0.8267 (ptm-80) cc_final: 0.8016 (ttp80) REVERT: B 525 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7184 (m-80) REVERT: B 563 SER cc_start: 0.7967 (p) cc_final: 0.7694 (p) REVERT: B 696 ILE cc_start: 0.8434 (mt) cc_final: 0.8221 (mm) REVERT: E 16 CYS cc_start: 0.5756 (m) cc_final: 0.5360 (t) REVERT: E 40 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7702 (mt-10) REVERT: E 78 ASP cc_start: 0.8082 (OUTLIER) cc_final: 0.7821 (t0) REVERT: E 82 MET cc_start: 0.6520 (mtm) cc_final: 0.5377 (pmm) REVERT: E 104 LYS cc_start: 0.8422 (tptt) cc_final: 0.7997 (mmmt) REVERT: E 158 GLU cc_start: 0.6152 (mp0) cc_final: 0.5860 (mp0) REVERT: E 172 GLU cc_start: 0.6510 (tm-30) cc_final: 0.6139 (tm-30) REVERT: E 173 MET cc_start: 0.8384 (tmm) cc_final: 0.8129 (ttt) REVERT: F 16 CYS cc_start: 0.5741 (m) cc_final: 0.5359 (t) REVERT: F 40 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7708 (mt-10) REVERT: F 78 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.7824 (t0) REVERT: F 82 MET cc_start: 0.6502 (mtm) cc_final: 0.5373 (pmm) REVERT: F 104 LYS cc_start: 0.8423 (tptt) cc_final: 0.7996 (mmmt) REVERT: F 173 MET cc_start: 0.8406 (tmm) cc_final: 0.8142 (tmm) outliers start: 58 outliers final: 40 residues processed: 389 average time/residue: 0.1439 time to fit residues: 90.9240 Evaluate side-chains 384 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 338 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 621 TYR Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 624 PHE Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 763 THR Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 782 GLU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 525 PHE Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 741 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 691 TYR Chi-restraints excluded: chain A residue 763 THR Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 78 ASP Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 78 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 20 optimal weight: 0.7980 chunk 270 optimal weight: 30.0000 chunk 209 optimal weight: 0.9980 chunk 253 optimal weight: 20.0000 chunk 220 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 233 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 138 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.189119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.135076 restraints weight = 34266.083| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 2.33 r_work: 0.3542 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22766 Z= 0.127 Angle : 0.596 12.425 30872 Z= 0.289 Chirality : 0.040 0.189 3536 Planarity : 0.004 0.050 3854 Dihedral : 7.843 130.190 3150 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.04 % Allowed : 17.58 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.16), residues: 2742 helix: 1.70 (0.13), residues: 1676 sheet: -0.19 (0.42), residues: 156 loop : -0.50 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 336 TYR 0.018 0.001 TYR D 621 PHE 0.025 0.001 PHE C 669 TRP 0.022 0.001 TRP C 785 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00296 (22762) covalent geometry : angle 0.59573 (30864) SS BOND : bond 0.00102 ( 4) SS BOND : angle 0.16210 ( 8) hydrogen bonds : bond 0.03215 ( 1243) hydrogen bonds : angle 4.13929 ( 3621) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5484 Ramachandran restraints generated. 2742 Oldfield, 0 Emsley, 2742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 350 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 225 GLU cc_start: 0.6602 (tp30) cc_final: 0.6249 (tp30) REVERT: C 457 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7971 (mp0) REVERT: C 511 LEU cc_start: 0.7597 (tp) cc_final: 0.7287 (tp) REVERT: C 621 TYR cc_start: 0.7132 (OUTLIER) cc_final: 0.6342 (t80) REVERT: C 703 ILE cc_start: 0.8943 (mt) cc_final: 0.8659 (pt) REVERT: D 223 MET cc_start: 0.7921 (tpp) cc_final: 0.7594 (tpp) REVERT: D 225 GLU cc_start: 0.8385 (mt-10) cc_final: 0.8031 (pt0) REVERT: D 387 GLN cc_start: 0.8380 (mt0) cc_final: 0.8049 (mt0) REVERT: D 400 ARG cc_start: 0.8205 (ptm-80) cc_final: 0.7940 (ttp80) REVERT: D 449 MET cc_start: 0.8735 (mtt) cc_final: 0.8448 (mtm) REVERT: D 525 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7058 (m-80) REVERT: D 555 ILE cc_start: 0.8543 (mm) cc_final: 0.8329 (mm) REVERT: D 563 SER cc_start: 0.7865 (p) cc_final: 0.7572 (p) REVERT: D 696 ILE cc_start: 0.8383 (mm) cc_final: 0.8115 (mt) REVERT: A 225 GLU cc_start: 0.6602 (tp30) cc_final: 0.6252 (tp30) REVERT: A 457 GLU cc_start: 0.8411 (mm-30) cc_final: 0.7970 (mp0) REVERT: A 511 LEU cc_start: 0.7597 (tp) cc_final: 0.7286 (tp) REVERT: A 621 TYR cc_start: 0.7130 (OUTLIER) cc_final: 0.6338 (t80) REVERT: A 703 ILE cc_start: 0.8874 (mt) cc_final: 0.8617 (pt) REVERT: B 223 MET cc_start: 0.7911 (tpp) cc_final: 0.7588 (tpp) REVERT: B 225 GLU cc_start: 0.8380 (mt-10) cc_final: 0.8026 (pt0) REVERT: B 387 GLN cc_start: 0.8372 (mt0) cc_final: 0.8051 (mt0) REVERT: B 400 ARG cc_start: 0.8208 (ptm-80) cc_final: 0.7947 (ttp80) REVERT: B 525 PHE cc_start: 0.7942 (OUTLIER) cc_final: 0.7162 (m-80) REVERT: B 563 SER cc_start: 0.7928 (p) cc_final: 0.7657 (p) REVERT: B 625 MET cc_start: 0.8356 (ttm) cc_final: 0.7790 (ttp) REVERT: B 696 ILE cc_start: 0.8410 (mt) cc_final: 0.8206 (mm) REVERT: E 16 CYS cc_start: 0.5893 (m) cc_final: 0.5513 (t) REVERT: E 40 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7720 (mt-10) REVERT: E 82 MET cc_start: 0.6582 (mtm) cc_final: 0.5404 (pmm) REVERT: E 104 LYS cc_start: 0.8480 (tptt) cc_final: 0.8071 (mmmt) REVERT: E 172 GLU cc_start: 0.6632 (tm-30) cc_final: 0.6253 (tm-30) REVERT: E 173 MET cc_start: 0.8395 (tmm) cc_final: 0.8167 (ttt) REVERT: F 16 CYS cc_start: 0.5876 (m) cc_final: 0.5514 (t) REVERT: F 40 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7714 (mt-10) REVERT: F 82 MET cc_start: 0.6572 (mtm) cc_final: 0.5417 (pmm) REVERT: F 104 LYS cc_start: 0.8485 (tptt) cc_final: 0.8067 (mmmt) REVERT: F 173 MET cc_start: 0.8439 (tmm) cc_final: 0.8162 (tmm) outliers start: 49 outliers final: 39 residues processed: 378 average time/residue: 0.1375 time to fit residues: 84.7949 Evaluate side-chains 390 residues out of total 2440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 347 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 314 MET Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 621 TYR Chi-restraints excluded: chain C residue 622 LEU Chi-restraints excluded: chain C residue 624 PHE Chi-restraints excluded: chain C residue 683 LEU Chi-restraints excluded: chain C residue 691 TYR Chi-restraints excluded: chain C residue 764 VAL Chi-restraints excluded: chain C residue 782 GLU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 194 CYS Chi-restraints excluded: chain D residue 195 LEU Chi-restraints excluded: chain D residue 295 THR Chi-restraints excluded: chain D residue 393 GLU Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 525 PHE Chi-restraints excluded: chain D residue 609 ILE Chi-restraints excluded: chain D residue 741 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 223 MET Chi-restraints excluded: chain A residue 250 CYS Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 621 TYR Chi-restraints excluded: chain A residue 622 LEU Chi-restraints excluded: chain A residue 624 PHE Chi-restraints excluded: chain A residue 691 TYR Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 782 GLU Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 194 CYS Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 393 GLU Chi-restraints excluded: chain B residue 504 THR Chi-restraints excluded: chain B residue 525 PHE Chi-restraints excluded: chain B residue 609 ILE Chi-restraints excluded: chain B residue 741 ILE Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain F residue 37 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 103 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 246 optimal weight: 10.0000 chunk 238 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 6.9990 chunk 184 optimal weight: 0.8980 chunk 145 optimal weight: 0.2980 chunk 111 optimal weight: 0.8980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 447 HIS A 447 HIS ** B 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.186592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.136980 restraints weight = 34250.838| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.56 r_work: 0.3462 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22766 Z= 0.172 Angle : 0.630 12.340 30872 Z= 0.309 Chirality : 0.041 0.189 3536 Planarity : 0.004 0.049 3854 Dihedral : 7.840 127.299 3150 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.91 % Allowed : 17.50 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.16), residues: 2742 helix: 1.58 (0.13), residues: 1676 sheet: -0.17 (0.41), residues: 158 loop : -0.59 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 753 TYR 0.012 0.001 TYR D 621 PHE 0.049 0.002 PHE C 669 TRP 0.024 0.002 TRP C 785 HIS 0.006 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00413 (22762) covalent geometry : angle 0.63055 (30864) SS BOND : bond 0.00193 ( 4) SS BOND : angle 0.23029 ( 8) hydrogen bonds : bond 0.03517 ( 1243) hydrogen bonds : angle 4.22912 ( 3621) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5568.47 seconds wall clock time: 96 minutes 13.14 seconds (5773.14 seconds total)