Starting phenix.real_space_refine on Fri Aug 7 11:00:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/11gq_75682/08_2026/11gq_75682.cif Found real_map, /net/cci-nas-00/data/ceres_data/11gq_75682/08_2026/11gq_75682.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/11gq_75682/08_2026/11gq_75682.cif" } default_model = "/net/cci-nas-00/data/ceres_data/11gq_75682/08_2026/11gq_75682.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/11gq_75682/08_2026/11gq_75682.map" default_real_map = "/net/cci-nas-00/data/ceres_data/11gq_75682/08_2026/11gq_75682.map" } resolution = 3.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 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 12 5.49 5 Mg 16 5.21 5 S 112 5.16 5 C 13186 2.51 5 N 3364 2.21 5 O 3946 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20636 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5072 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 616} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 5036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5036 Classifications: {'peptide': 637} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 21, 'TRANS': 615} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5072 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 616} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 5036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5036 Classifications: {'peptide': 637} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 21, 'TRANS': 615} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 49 Unusual residues: {' MG': 4, 'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 49 Unusual residues: {' MG': 4, 'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 49 Unusual residues: {' MG': 4, 'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 49 Unusual residues: {' MG': 4, 'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.33, per 1000 atoms: 0.21 Number of scatterers: 20636 At special positions: 0 Unit cell: (119.053, 131.219, 228.547, 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 112 16.00 P 12 15.00 Mg 16 11.99 O 3946 8.00 N 3364 7.00 C 13186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 58 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 151 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 58 " distance=2.02 Simple disulfide: pdb=" SG CYS B 108 " - pdb=" SG CYS B 151 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 58 " distance=2.03 Simple disulfide: pdb=" SG CYS C 108 " - pdb=" SG CYS C 151 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 58 " distance=2.03 Simple disulfide: pdb=" SG CYS D 108 " - pdb=" SG CYS D 151 " 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A 906 " - " ASN A 127 " " NAG B 906 " - " ASN B 127 " " NAG C 906 " - " ASN C 127 " " NAG D 906 " - " ASN D 127 " " NAG E 1 " - " ASN A 55 " " NAG F 1 " - " ASN A 122 " " NAG G 1 " - " ASN B 55 " " NAG H 1 " - " ASN B 122 " " NAG I 1 " - " ASN C 55 " " NAG J 1 " - " ASN C 122 " " NAG K 1 " - " ASN D 55 " " NAG L 1 " - " ASN D 122 " Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 655.1 milliseconds 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4836 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 36 sheets defined 47.9% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 98 through 105 removed outlier: 3.780A pdb=" N HIS A 103 " --> pdb=" O ALA A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 181 through 208 Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 222 through 239 Proline residue: A 234 - end of helix removed outlier: 4.055A pdb=" N LYS A 238 " --> pdb=" O PRO A 234 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 265 Processing helix chain 'A' and resid 268 through 284 Processing helix chain 'A' and resid 284 through 294 Processing helix chain 'A' and resid 294 through 302 Processing helix chain 'A' and resid 302 through 313 Processing helix chain 'A' and resid 313 through 329 Proline residue: A 319 - end of helix Processing helix chain 'A' and resid 337 through 349 Processing helix chain 'A' and resid 355 through 368 Processing helix chain 'A' and resid 372 through 376 Processing helix chain 'A' and resid 393 through 404 removed outlier: 3.928A pdb=" N GLY A 404 " --> pdb=" O ILE A 400 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 428 Processing helix chain 'A' and resid 431 through 435 removed outlier: 3.604A pdb=" N CYS A 435 " --> pdb=" O PRO A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 446 Processing helix chain 'A' and resid 457 through 468 removed outlier: 3.670A pdb=" N GLY A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 504 Processing helix chain 'A' and resid 547 through 562 removed outlier: 3.708A pdb=" N VAL A 562 " --> pdb=" O LEU A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 580 Processing helix chain 'A' and resid 641 through 646 removed outlier: 3.913A pdb=" N THR A 645 " --> pdb=" O THR A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 728 removed outlier: 4.160A pdb=" N ASN A 727 " --> pdb=" O SER A 723 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N SER A 728 " --> pdb=" O ARG A 724 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 105 removed outlier: 3.520A pdb=" N HIS B 103 " --> pdb=" O ALA B 99 " (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 181 through 209 removed outlier: 4.070A pdb=" N MET B 207 " --> pdb=" O ASN B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 222 through 238 Proline residue: B 234 - end of helix removed outlier: 4.101A pdb=" N LYS B 238 " --> pdb=" O PRO B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 265 Processing helix chain 'B' and resid 268 through 284 Processing helix chain 'B' and resid 285 through 294 Processing helix chain 'B' and resid 294 through 302 Processing helix chain 'B' and resid 302 through 313 Processing helix chain 'B' and resid 313 through 329 Proline residue: B 319 - end of helix Processing helix chain 'B' and resid 337 through 349 Processing helix chain 'B' and resid 350 through 352 No H-bonds generated for 'chain 'B' and resid 350 through 352' Processing helix chain 'B' and resid 355 through 368 Processing helix chain 'B' and resid 372 through 377 removed outlier: 4.057A pdb=" N ILE B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 404 removed outlier: 3.659A pdb=" N GLY B 404 " --> pdb=" O ILE B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 428 Processing helix chain 'B' and resid 431 through 435 Processing helix chain 'B' and resid 438 through 446 Processing helix chain 'B' and resid 457 through 468 removed outlier: 3.772A pdb=" N GLY B 468 " --> pdb=" O GLU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 505 Processing helix chain 'B' and resid 528 through 539 Processing helix chain 'B' and resid 547 through 561 Processing helix chain 'B' and resid 571 through 581 Processing helix chain 'B' and resid 597 through 601 removed outlier: 3.595A pdb=" N TYR B 601 " --> pdb=" O ALA B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 646 removed outlier: 4.431A pdb=" N THR B 645 " --> pdb=" O THR B 641 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER B 646 " --> pdb=" O MET B 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 641 through 646' Processing helix chain 'B' and resid 713 through 728 Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 98 through 105 removed outlier: 3.779A pdb=" N HIS C 103 " --> pdb=" O ALA C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 181 through 208 Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 222 through 239 Proline residue: C 234 - end of helix removed outlier: 4.056A pdb=" N LYS C 238 " --> pdb=" O PRO C 234 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 239 through 265 Processing helix chain 'C' and resid 268 through 284 Processing helix chain 'C' and resid 284 through 294 Processing helix chain 'C' and resid 294 through 302 Processing helix chain 'C' and resid 302 through 313 Processing helix chain 'C' and resid 313 through 329 Proline residue: C 319 - end of helix Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 355 through 368 Processing helix chain 'C' and resid 372 through 376 Processing helix chain 'C' and resid 393 through 404 removed outlier: 3.926A pdb=" N GLY C 404 " --> pdb=" O ILE C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 428 Processing helix chain 'C' and resid 431 through 435 removed outlier: 3.599A pdb=" N CYS C 435 " --> pdb=" O PRO C 432 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 446 Processing helix chain 'C' and resid 457 through 468 removed outlier: 3.669A pdb=" N GLY C 468 " --> pdb=" O GLU C 464 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 504 Processing helix chain 'C' and resid 547 through 562 removed outlier: 3.712A pdb=" N VAL C 562 " --> pdb=" O LEU C 558 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 580 Processing helix chain 'C' and resid 641 through 646 removed outlier: 3.911A pdb=" N THR C 645 " --> pdb=" O THR C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 728 removed outlier: 4.159A pdb=" N ASN C 727 " --> pdb=" O SER C 723 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N SER C 728 " --> pdb=" O ARG C 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 105 removed outlier: 3.521A pdb=" N HIS D 103 " --> pdb=" O ALA D 99 " (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 181 through 209 removed outlier: 4.072A pdb=" N MET D 207 " --> pdb=" O ASN D 203 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 220 Processing helix chain 'D' and resid 222 through 238 Proline residue: D 234 - end of helix removed outlier: 4.103A pdb=" N LYS D 238 " --> pdb=" O PRO D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 265 Processing helix chain 'D' and resid 268 through 284 Processing helix chain 'D' and resid 285 through 294 Processing helix chain 'D' and resid 294 through 302 Processing helix chain 'D' and resid 302 through 313 Processing helix chain 'D' and resid 313 through 329 Proline residue: D 319 - end of helix Processing helix chain 'D' and resid 337 through 349 Processing helix chain 'D' and resid 350 through 352 No H-bonds generated for 'chain 'D' and resid 350 through 352' Processing helix chain 'D' and resid 355 through 368 Processing helix chain 'D' and resid 372 through 377 removed outlier: 4.056A pdb=" N ILE D 376 " --> pdb=" O THR D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.657A pdb=" N GLY D 404 " --> pdb=" O ILE D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 428 Processing helix chain 'D' and resid 431 through 435 Processing helix chain 'D' and resid 438 through 446 Processing helix chain 'D' and resid 457 through 468 removed outlier: 3.773A pdb=" N GLY D 468 " --> pdb=" O GLU D 464 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 505 Processing helix chain 'D' and resid 528 through 539 Processing helix chain 'D' and resid 547 through 561 Processing helix chain 'D' and resid 571 through 581 Processing helix chain 'D' and resid 597 through 601 removed outlier: 3.597A pdb=" N TYR D 601 " --> pdb=" O ALA D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 641 through 646 removed outlier: 4.432A pdb=" N THR D 645 " --> pdb=" O THR D 641 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER D 646 " --> pdb=" O MET D 642 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 641 through 646' Processing helix chain 'D' and resid 713 through 728 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 54 removed outlier: 6.586A pdb=" N TYR A 79 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N MET A 49 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ARG A 77 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N LEU A 51 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ASN A 75 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER A 53 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N THR A 73 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N SER A 129 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASN A 122 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N VAL A 131 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU A 120 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL A 133 " --> pdb=" O GLN A 118 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.540A pdb=" N ILE A 66 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL A 173 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL A 68 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 58 through 60 removed outlier: 6.540A pdb=" N ILE A 66 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL A 173 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N VAL A 68 " --> pdb=" O VAL A 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 378 through 379 removed outlier: 6.510A pdb=" N TYR A 488 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASN A 479 " --> pdb=" O TYR A 488 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N VAL A 490 " --> pdb=" O LYS A 477 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LYS A 477 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N HIS A 450 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N GLN A 476 " --> pdb=" O HIS A 450 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL A 452 " --> pdb=" O GLN A 476 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N VAL A 478 " --> pdb=" O VAL A 452 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 387 Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 392 removed outlier: 4.272A pdb=" N THR A 436 " --> pdb=" O LEU A 392 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 585 through 588 removed outlier: 6.408A pdb=" N GLN A 707 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 637 " --> pdb=" O ILE A 615 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 607 through 608 removed outlier: 3.956A pdb=" N LYS A 607 " --> pdb=" O SER A 696 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 629 through 633 Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 54 removed outlier: 5.281A pdb=" N ILE B 46 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR B 81 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY B 48 " --> pdb=" O TYR B 79 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASN B 75 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N CYS B 54 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N THR B 73 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER B 129 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL B 123 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN B 119 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LEU B 135 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL B 117 " --> pdb=" O LEU B 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.502A pdb=" N ILE B 66 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL B 173 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL B 68 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 58 through 60 removed outlier: 6.502A pdb=" N ILE B 66 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N VAL B 173 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL B 68 " --> pdb=" O VAL B 173 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 378 through 379 removed outlier: 3.669A pdb=" N PHE B 487 " --> pdb=" O ASN B 479 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL B 475 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU B 493 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA B 473 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N HIS B 450 " --> pdb=" O LEU B 472 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 386 through 387 removed outlier: 6.252A pdb=" N ILE B 408 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ILE B 421 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL B 410 " --> pdb=" O VAL B 419 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 391 through 392 removed outlier: 3.875A pdb=" N THR B 436 " --> pdb=" O LEU B 392 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 585 through 588 removed outlier: 6.464A pdb=" N GLN B 707 " --> pdb=" O LEU B 616 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 607 through 608 removed outlier: 3.873A pdb=" N LYS B 607 " --> pdb=" O SER B 696 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 629 through 633 Processing sheet with id=AC1, first strand: chain 'C' and resid 45 through 54 removed outlier: 6.591A pdb=" N TYR C 79 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N MET C 49 " --> pdb=" O ARG C 77 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARG C 77 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N LEU C 51 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ASN C 75 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N SER C 53 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR C 73 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER C 129 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ASN C 122 " --> pdb=" O SER C 129 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N VAL C 131 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU C 120 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N VAL C 133 " --> pdb=" O GLN C 118 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.537A pdb=" N ILE C 66 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL C 173 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL C 68 " --> pdb=" O VAL C 173 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 58 through 60 removed outlier: 6.537A pdb=" N ILE C 66 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL C 173 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N VAL C 68 " --> pdb=" O VAL C 173 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 378 through 379 removed outlier: 6.509A pdb=" N TYR C 488 " --> pdb=" O ASN C 479 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN C 479 " --> pdb=" O TYR C 488 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N VAL C 490 " --> pdb=" O LYS C 477 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS C 477 " --> pdb=" O VAL C 490 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N HIS C 450 " --> pdb=" O ILE C 474 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N GLN C 476 " --> pdb=" O HIS C 450 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VAL C 452 " --> pdb=" O GLN C 476 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N VAL C 478 " --> pdb=" O VAL C 452 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 386 through 387 Processing sheet with id=AC6, first strand: chain 'C' and resid 391 through 392 removed outlier: 4.274A pdb=" N THR C 436 " --> pdb=" O LEU C 392 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 585 through 588 removed outlier: 6.408A pdb=" N GLN C 707 " --> pdb=" O LEU C 616 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N SER C 637 " --> pdb=" O ILE C 615 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 607 through 608 removed outlier: 3.956A pdb=" N LYS C 607 " --> pdb=" O SER C 696 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 629 through 633 Processing sheet with id=AD1, first strand: chain 'D' and resid 45 through 54 removed outlier: 5.281A pdb=" N ILE D 46 " --> pdb=" O TYR D 81 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR D 81 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY D 48 " --> pdb=" O TYR D 79 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ASN D 75 " --> pdb=" O ALA D 52 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N CYS D 54 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR D 73 " --> pdb=" O CYS D 54 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N SER D 129 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N VAL D 123 " --> pdb=" O SER D 129 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN D 119 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU D 135 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N VAL D 117 " --> pdb=" O LEU D 135 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.515A pdb=" N ILE D 66 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL D 173 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL D 68 " --> pdb=" O VAL D 173 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 58 through 60 removed outlier: 6.515A pdb=" N ILE D 66 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N VAL D 173 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL D 68 " --> pdb=" O VAL D 173 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 378 through 379 removed outlier: 3.668A pdb=" N PHE D 487 " --> pdb=" O ASN D 479 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL D 475 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU D 493 " --> pdb=" O ALA D 473 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA D 473 " --> pdb=" O LEU D 493 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N HIS D 450 " --> pdb=" O LEU D 472 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 386 through 387 removed outlier: 6.252A pdb=" N ILE D 408 " --> pdb=" O ILE D 421 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ILE D 421 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL D 410 " --> pdb=" O VAL D 419 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 391 through 392 removed outlier: 3.874A pdb=" N THR D 436 " --> pdb=" O LEU D 392 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 585 through 588 removed outlier: 6.464A pdb=" N GLN D 707 " --> pdb=" O LEU D 616 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 607 through 608 removed outlier: 3.871A pdb=" N LYS D 607 " --> pdb=" O SER D 696 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 629 through 633 1028 hydrogen bonds defined for protein. 2934 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: 3.83 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6536 1.34 - 1.46: 3344 1.46 - 1.57: 10900 1.57 - 1.69: 14 1.69 - 1.81: 188 Bond restraints: 20982 Sorted by residual: bond pdb=" CB VAL A 373 " pdb=" CG1 VAL A 373 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.49e+00 bond pdb=" CB VAL C 373 " pdb=" CG1 VAL C 373 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.47e+00 bond pdb=" C PRO B 176 " pdb=" N GLY B 177 " ideal model delta sigma weight residual 1.331 1.308 0.023 1.46e-02 4.69e+03 2.40e+00 bond pdb=" CB VAL B 280 " pdb=" CG2 VAL B 280 " ideal model delta sigma weight residual 1.521 1.470 0.051 3.30e-02 9.18e+02 2.34e+00 bond pdb=" CG1 ILE C 408 " pdb=" CD1 ILE C 408 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.28e+00 ... (remaining 20977 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 26972 1.18 - 2.37: 1138 2.37 - 3.55: 228 3.55 - 4.74: 60 4.74 - 5.92: 16 Bond angle restraints: 28414 Sorted by residual: angle pdb=" N SER D 87 " pdb=" CA SER D 87 " pdb=" C SER D 87 " ideal model delta sigma weight residual 112.12 115.28 -3.16 1.34e+00 5.57e-01 5.57e+00 angle pdb=" N SER B 87 " pdb=" CA SER B 87 " pdb=" C SER B 87 " ideal model delta sigma weight residual 112.12 115.27 -3.15 1.34e+00 5.57e-01 5.54e+00 angle pdb=" N GLY B 266 " pdb=" CA GLY B 266 " pdb=" C GLY B 266 " ideal model delta sigma weight residual 111.56 113.84 -2.28 1.01e+00 9.80e-01 5.10e+00 angle pdb=" N GLY D 266 " pdb=" CA GLY D 266 " pdb=" C GLY D 266 " ideal model delta sigma weight residual 111.56 113.82 -2.26 1.01e+00 9.80e-01 5.02e+00 angle pdb=" C ASN B 203 " pdb=" N LEU B 204 " pdb=" CA LEU B 204 " ideal model delta sigma weight residual 120.71 117.08 3.63 1.67e+00 3.59e-01 4.72e+00 ... (remaining 28409 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.09: 11833 12.09 - 24.17: 942 24.17 - 36.26: 194 36.26 - 48.34: 78 48.34 - 60.43: 39 Dihedral angle restraints: 13086 sinusoidal: 5618 harmonic: 7468 Sorted by residual: dihedral pdb=" CA LEU D 706 " pdb=" C LEU D 706 " pdb=" N GLN D 707 " pdb=" CA GLN D 707 " ideal model delta harmonic sigma weight residual 180.00 163.40 16.60 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA LEU B 706 " pdb=" C LEU B 706 " pdb=" N GLN B 707 " pdb=" CA GLN B 707 " ideal model delta harmonic sigma weight residual 180.00 163.42 16.58 0 5.00e+00 4.00e-02 1.10e+01 dihedral pdb=" CA MET A 49 " pdb=" C MET A 49 " pdb=" N ARG A 50 " pdb=" CA ARG A 50 " ideal model delta harmonic sigma weight residual 180.00 163.62 16.38 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 13083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 3203 0.094 - 0.188: 187 0.188 - 0.281: 0 0.281 - 0.375: 0 0.375 - 0.469: 4 Chirality restraints: 3394 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.37e+01 chirality pdb=" C1 NAG K 2 " pdb=" O4 NAG K 1 " pdb=" C2 NAG K 2 " pdb=" O5 NAG K 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.22 -0.18 2.00e-02 2.50e+03 8.16e+01 chirality pdb=" C1 NAG L 2 " pdb=" O4 NAG L 1 " pdb=" C2 NAG L 2 " pdb=" O5 NAG L 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.33 -0.07 2.00e-02 2.50e+03 1.33e+01 ... (remaining 3391 not shown) Planarity restraints: 3544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 141 " 0.195 9.50e-02 1.11e+02 8.78e-02 5.15e+00 pdb=" NE ARG A 141 " -0.015 2.00e-02 2.50e+03 pdb=" CZ ARG A 141 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 141 " -0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 141 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 141 " -0.190 9.50e-02 1.11e+02 8.54e-02 4.92e+00 pdb=" NE ARG C 141 " 0.015 2.00e-02 2.50e+03 pdb=" CZ ARG C 141 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG C 141 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 141 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 612 " 0.015 2.00e-02 2.50e+03 1.17e-02 2.38e+00 pdb=" CG PHE C 612 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE C 612 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C 612 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 612 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 612 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE C 612 " 0.004 2.00e-02 2.50e+03 ... (remaining 3541 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 480 2.71 - 3.26: 20700 3.26 - 3.80: 31995 3.80 - 4.35: 41217 4.35 - 4.90: 71363 Nonbonded interactions: 165755 Sorted by model distance: nonbonded pdb=" OD2 ASP C 510 " pdb="MG MG C 902 " model vdw 2.159 2.170 nonbonded pdb=" OD2 ASP A 510 " pdb="MG MG A 902 " model vdw 2.170 2.170 nonbonded pdb=" NH1 ARG B 369 " pdb=" OD2 ASP B 459 " model vdw 2.235 3.120 nonbonded pdb=" NH1 ARG D 369 " pdb=" OD2 ASP D 459 " model vdw 2.237 3.120 nonbonded pdb=" OE2 GLU B 501 " pdb="MG MG B 903 " model vdw 2.261 2.170 ... (remaining 165750 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 'A' and (resid 44 through 518 or (resid 519 and (name N or name CA or nam \ e C or name O or name CB )) or resid 520 or (resid 521 through 523 and (name N o \ r name CA or name C or name O or name CB )) or resid 524 through 529 or (resid 5 \ 30 and (name N or name CA or name C or name O or name CB )) or resid 531 through \ 647 or resid 693 through 906)) selection = (chain 'B' and (resid 44 through 527 or (resid 528 through 530 and (name N or na \ me CA or name C or name O or name CB )) or resid 531 through 906)) selection = (chain 'C' and (resid 44 through 518 or (resid 519 and (name N or name CA or nam \ e C or name O or name CB )) or resid 520 or (resid 521 through 523 and (name N o \ r name CA or name C or name O or name CB )) or resid 524 through 529 or (resid 5 \ 30 and (name N or name CA or name C or name O or name CB )) or resid 531 through \ 647 or resid 693 through 906)) selection = (chain 'D' and (resid 44 through 527 or (resid 528 through 530 and (name N or na \ me CA or name C or name O or name CB )) or resid 531 through 906)) } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.000 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.060 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:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6896 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 : 0.007 0.059 21010 Z= 0.304 Angle : 0.635 9.610 28490 Z= 0.323 Chirality : 0.049 0.469 3394 Planarity : 0.004 0.088 3532 Dihedral : 10.174 60.429 8226 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.84 % Allowed : 4.31 % Favored : 94.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.17), residues: 2528 helix: 1.66 (0.16), residues: 1024 sheet: -1.06 (0.24), residues: 418 loop : -0.42 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 141 TYR 0.023 0.002 TYR C 638 PHE 0.026 0.002 PHE C 612 TRP 0.007 0.001 TRP C 183 HIS 0.006 0.001 HIS C 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00718 / 0.30 (20982) covalent geometry : angle 0.60857 / 0.32 (28414) SS BOND : bond 0.00390 / 0.24 ( 8) SS BOND : angle 0.49291 / 0.32 ( 16) hydrogen bonds : bond 0.10661 / 7.23 ( 1004) hydrogen bonds : angle 6.49937 / 4.65 ( 2934) link_BETA1-4 : bond 0.00326 / 0.22 ( 8) link_BETA1-4 : angle 4.98124 / 3.32 ( 24) link_NAG-ASN : bond 0.00388 / 0.27 ( 12) link_NAG-ASN : angle 3.21202 / 2.66 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 316 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 385 MET cc_start: 0.5921 (mtp) cc_final: 0.5689 (mtp) REVERT: D 397 MET cc_start: 0.6723 (mtp) cc_final: 0.6427 (mtp) outliers start: 19 outliers final: 6 residues processed: 333 average time/residue: 0.1353 time to fit residues: 68.9307 Evaluate side-chains 174 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 168 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 351 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 0.6980 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN A 254 ASN A 600 HIS B 89 ASN B 103 HIS B 254 ASN B 263 ASN B 540 ASN C 85 ASN C 254 ASN C 600 HIS C 606 ASN D 89 ASN D 103 HIS D 254 ASN D 263 ASN D 528 ASN D 540 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.068807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.052033 restraints weight = 83100.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.054042 restraints weight = 42346.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.055318 restraints weight = 28943.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.056084 restraints weight = 23084.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.056616 restraints weight = 20168.770| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21010 Z= 0.137 Angle : 0.630 14.140 28490 Z= 0.304 Chirality : 0.043 0.345 3394 Planarity : 0.004 0.060 3532 Dihedral : 6.995 63.356 3308 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.41 % Allowed : 8.75 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.17), residues: 2528 helix: 2.03 (0.16), residues: 1036 sheet: -0.88 (0.25), residues: 414 loop : -0.06 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 599 TYR 0.007 0.001 TYR B 597 PHE 0.016 0.001 PHE C 612 TRP 0.020 0.001 TRP B 160 HIS 0.004 0.001 HIS A 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (20982) covalent geometry : angle 0.61362 / 0.30 (28414) SS BOND : bond 0.00248 / 0.17 ( 8) SS BOND : angle 0.48630 / 0.31 ( 16) hydrogen bonds : bond 0.03842 / 2.55 ( 1004) hydrogen bonds : angle 5.21176 / 3.75 ( 2934) link_BETA1-4 : bond 0.00448 / 0.27 ( 8) link_BETA1-4 : angle 3.64877 / 2.47 ( 24) link_NAG-ASN : bond 0.00370 / 0.26 ( 12) link_NAG-ASN : angle 2.87476 / 2.32 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.773 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: A 401 MET cc_start: 0.9287 (mmm) cc_final: 0.9024 (mmm) REVERT: A 461 MET cc_start: 0.9019 (tpp) cc_final: 0.8811 (tpp) REVERT: C 401 MET cc_start: 0.9317 (mmm) cc_final: 0.9024 (mmm) REVERT: C 412 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7548 (tm-30) REVERT: C 413 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7544 (m-30) REVERT: D 160 TRP cc_start: 0.7205 (m100) cc_final: 0.6574 (m100) REVERT: D 270 MET cc_start: 0.5680 (tmm) cc_final: 0.5428 (tmm) outliers start: 32 outliers final: 16 residues processed: 212 average time/residue: 0.1182 time to fit residues: 41.1558 Evaluate side-chains 167 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 TYR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain C residue 279 ILE Chi-restraints excluded: chain C residue 290 LEU Chi-restraints excluded: chain C residue 413 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 504 ILE Chi-restraints excluded: chain D residue 531 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 205 optimal weight: 0.7980 chunk 184 optimal weight: 0.8980 chunk 217 optimal weight: 9.9990 chunk 208 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 41 optimal weight: 0.7980 chunk 149 optimal weight: 0.9980 chunk 38 optimal weight: 0.0060 chunk 220 optimal weight: 4.9990 chunk 126 optimal weight: 10.0000 chunk 152 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 606 ASN B 185 HIS ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.068840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.051992 restraints weight = 83949.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.054007 restraints weight = 42908.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.055292 restraints weight = 29216.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.056078 restraints weight = 23255.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.056581 restraints weight = 20263.538| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21010 Z= 0.119 Angle : 0.577 9.307 28490 Z= 0.280 Chirality : 0.042 0.332 3394 Planarity : 0.003 0.040 3532 Dihedral : 6.787 64.449 3306 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.10 % Allowed : 10.55 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.17), residues: 2528 helix: 2.20 (0.16), residues: 1050 sheet: -0.80 (0.26), residues: 392 loop : 0.11 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 140 TYR 0.025 0.001 TYR D 597 PHE 0.014 0.001 PHE A 612 TRP 0.009 0.001 TRP B 160 HIS 0.004 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (20982) covalent geometry : angle 0.56013 / 0.28 (28414) SS BOND : bond 0.00218 / 0.15 ( 8) SS BOND : angle 0.44828 / 0.28 ( 16) hydrogen bonds : bond 0.03522 / 2.34 ( 1004) hydrogen bonds : angle 4.92369 / 3.55 ( 2934) link_BETA1-4 : bond 0.00435 / 0.31 ( 8) link_BETA1-4 : angle 3.55837 / 2.40 ( 24) link_NAG-ASN : bond 0.00364 / 0.26 ( 12) link_NAG-ASN : angle 2.72037 / 2.20 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 161 time to evaluate : 0.830 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: A 401 MET cc_start: 0.9290 (mmm) cc_final: 0.9049 (mmm) REVERT: A 413 ASP cc_start: 0.7412 (m-30) cc_final: 0.6982 (m-30) REVERT: B 377 MET cc_start: 0.8513 (ttp) cc_final: 0.8233 (ttp) REVERT: C 286 LEU cc_start: 0.9151 (mm) cc_final: 0.8868 (mt) REVERT: C 401 MET cc_start: 0.9327 (mmm) cc_final: 0.9043 (mmm) REVERT: C 412 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7799 (tm-30) REVERT: C 413 ASP cc_start: 0.7693 (t0) cc_final: 0.7397 (m-30) REVERT: C 461 MET cc_start: 0.9019 (tpp) cc_final: 0.8787 (tpp) REVERT: D 160 TRP cc_start: 0.7307 (m100) cc_final: 0.6861 (m100) REVERT: D 270 MET cc_start: 0.5671 (tmm) cc_final: 0.5442 (tmm) REVERT: D 377 MET cc_start: 0.8566 (ttp) cc_final: 0.8248 (ttp) outliers start: 25 outliers final: 15 residues processed: 183 average time/residue: 0.1259 time to fit residues: 37.8677 Evaluate side-chains 165 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 TYR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 504 ILE Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 531 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 108 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 153 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 233 optimal weight: 7.9990 chunk 114 optimal weight: 1.9990 chunk 205 optimal weight: 5.9990 chunk 119 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 606 ASN B 263 ASN B 381 GLN ** C 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 381 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.066591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.049402 restraints weight = 84167.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.051337 restraints weight = 44234.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.052587 restraints weight = 30646.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.053353 restraints weight = 24597.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.053756 restraints weight = 21556.639| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21010 Z= 0.193 Angle : 0.609 7.432 28490 Z= 0.298 Chirality : 0.043 0.359 3394 Planarity : 0.003 0.041 3532 Dihedral : 6.740 64.418 3306 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.58 % Allowed : 11.08 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.17), residues: 2528 helix: 2.28 (0.16), residues: 1048 sheet: -0.85 (0.26), residues: 376 loop : 0.27 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 724 TYR 0.024 0.001 TYR B 597 PHE 0.024 0.001 PHE B 532 TRP 0.005 0.001 TRP A 160 HIS 0.003 0.001 HIS A 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.19 (20982) covalent geometry : angle 0.59564 / 0.30 (28414) SS BOND : bond 0.00291 / 0.19 ( 8) SS BOND : angle 0.41004 / 0.27 ( 16) hydrogen bonds : bond 0.03669 / 2.46 ( 1004) hydrogen bonds : angle 4.79617 / 3.47 ( 2934) link_BETA1-4 : bond 0.00525 / 0.32 ( 8) link_BETA1-4 : angle 3.21476 / 2.17 ( 24) link_NAG-ASN : bond 0.00243 / 0.17 ( 12) link_NAG-ASN : angle 2.63619 / 2.16 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 LEU cc_start: 0.9139 (mm) cc_final: 0.8937 (mt) REVERT: A 401 MET cc_start: 0.9269 (mmm) cc_final: 0.9022 (mmm) REVERT: B 377 MET cc_start: 0.8601 (ttp) cc_final: 0.8391 (ttp) REVERT: C 171 PHE cc_start: 0.8340 (OUTLIER) cc_final: 0.7733 (m-80) REVERT: C 401 MET cc_start: 0.9269 (mmm) cc_final: 0.9022 (mmm) REVERT: C 461 MET cc_start: 0.9030 (tpp) cc_final: 0.8822 (tpp) REVERT: C 642 MET cc_start: 0.8450 (mmm) cc_final: 0.8162 (mmt) REVERT: D 172 MET cc_start: 0.7411 (tpp) cc_final: 0.6956 (tpp) REVERT: D 189 ILE cc_start: 0.8887 (tp) cc_final: 0.8670 (tp) REVERT: D 377 MET cc_start: 0.8646 (ttp) cc_final: 0.8413 (ttp) outliers start: 36 outliers final: 23 residues processed: 187 average time/residue: 0.1358 time to fit residues: 41.7641 Evaluate side-chains 171 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 147 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 TYR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 531 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 94 optimal weight: 4.9990 chunk 203 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 226 optimal weight: 8.9990 chunk 192 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 22 optimal weight: 0.0770 chunk 56 optimal weight: 0.6980 chunk 133 optimal weight: 7.9990 chunk 61 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 overall best weight: 1.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 454 HIS D 454 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.066675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.049587 restraints weight = 83642.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.051483 restraints weight = 43756.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.052734 restraints weight = 30314.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.053472 restraints weight = 24342.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.053983 restraints weight = 21350.944| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21010 Z= 0.152 Angle : 0.572 8.828 28490 Z= 0.278 Chirality : 0.042 0.337 3394 Planarity : 0.003 0.034 3532 Dihedral : 6.658 63.963 3306 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.76 % Allowed : 12.05 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.46 (0.17), residues: 2528 helix: 2.33 (0.16), residues: 1056 sheet: -0.73 (0.27), residues: 368 loop : 0.35 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 338 TYR 0.014 0.001 TYR D 597 PHE 0.022 0.001 PHE B 532 TRP 0.004 0.001 TRP A 183 HIS 0.002 0.001 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (20982) covalent geometry : angle 0.55792 / 0.28 (28414) SS BOND : bond 0.00215 / 0.14 ( 8) SS BOND : angle 0.43271 / 0.27 ( 16) hydrogen bonds : bond 0.03412 / 2.28 ( 1004) hydrogen bonds : angle 4.66098 / 3.38 ( 2934) link_BETA1-4 : bond 0.00332 / 0.21 ( 8) link_BETA1-4 : angle 3.27261 / 2.21 ( 24) link_NAG-ASN : bond 0.00291 / 0.21 ( 12) link_NAG-ASN : angle 2.53895 / 2.09 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 LEU cc_start: 0.9123 (mm) cc_final: 0.8910 (mt) REVERT: A 401 MET cc_start: 0.9249 (mmm) cc_final: 0.9019 (mmm) REVERT: A 412 GLU cc_start: 0.7970 (tm-30) cc_final: 0.6122 (tm-30) REVERT: A 510 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8663 (t0) REVERT: B 172 MET cc_start: 0.7692 (tpp) cc_final: 0.7284 (tpp) REVERT: B 377 MET cc_start: 0.8670 (ttp) cc_final: 0.8463 (ttp) REVERT: C 171 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7828 (m-80) REVERT: C 401 MET cc_start: 0.9259 (mmm) cc_final: 0.9033 (mmm) REVERT: C 510 ASP cc_start: 0.8854 (OUTLIER) cc_final: 0.8605 (t0) REVERT: D 172 MET cc_start: 0.7566 (tpp) cc_final: 0.7056 (tpp) REVERT: D 377 MET cc_start: 0.8717 (ttp) cc_final: 0.8489 (ttp) outliers start: 40 outliers final: 25 residues processed: 195 average time/residue: 0.1301 time to fit residues: 41.8228 Evaluate side-chains 169 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 141 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 TYR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 510 ASP Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 531 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 64 optimal weight: 7.9990 chunk 144 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 166 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 30 optimal weight: 6.9990 chunk 146 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 159 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 606 ASN ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.066747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.049760 restraints weight = 83232.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.051702 restraints weight = 43402.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.052940 restraints weight = 29887.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.053716 restraints weight = 23960.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.054158 restraints weight = 20923.283| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21010 Z= 0.133 Angle : 0.583 10.172 28490 Z= 0.279 Chirality : 0.042 0.328 3394 Planarity : 0.003 0.034 3532 Dihedral : 6.619 63.317 3306 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.54 % Allowed : 12.62 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.17), residues: 2528 helix: 2.43 (0.16), residues: 1058 sheet: -0.67 (0.27), residues: 368 loop : 0.39 (0.20), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 599 TYR 0.025 0.001 TYR C 597 PHE 0.039 0.001 PHE D 532 TRP 0.003 0.000 TRP A 183 HIS 0.002 0.001 HIS D 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (20982) covalent geometry : angle 0.56919 / 0.28 (28414) SS BOND : bond 0.00204 / 0.13 ( 8) SS BOND : angle 0.40041 / 0.25 ( 16) hydrogen bonds : bond 0.03319 / 2.21 ( 1004) hydrogen bonds : angle 4.59702 / 3.33 ( 2934) link_BETA1-4 : bond 0.00375 / 0.24 ( 8) link_BETA1-4 : angle 3.24534 / 2.19 ( 24) link_NAG-ASN : bond 0.00314 / 0.22 ( 12) link_NAG-ASN : angle 2.47372 / 2.03 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 155 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 VAL cc_start: 0.8670 (OUTLIER) cc_final: 0.8458 (t) REVERT: A 286 LEU cc_start: 0.9104 (mm) cc_final: 0.8880 (mt) REVERT: A 401 MET cc_start: 0.9240 (mmm) cc_final: 0.9020 (mmm) REVERT: A 412 GLU cc_start: 0.7412 (tm-30) cc_final: 0.7081 (tm-30) REVERT: A 510 ASP cc_start: 0.8887 (OUTLIER) cc_final: 0.8594 (t0) REVERT: A 642 MET cc_start: 0.8403 (mmm) cc_final: 0.8080 (mmt) REVERT: B 172 MET cc_start: 0.7706 (tpp) cc_final: 0.7217 (tpp) REVERT: B 264 LEU cc_start: 0.8649 (tt) cc_final: 0.8133 (tp) REVERT: C 123 VAL cc_start: 0.8619 (OUTLIER) cc_final: 0.8416 (t) REVERT: C 171 PHE cc_start: 0.8419 (OUTLIER) cc_final: 0.8000 (m-80) REVERT: C 401 MET cc_start: 0.9252 (mmm) cc_final: 0.9032 (mmm) REVERT: C 510 ASP cc_start: 0.8874 (OUTLIER) cc_final: 0.8551 (t0) REVERT: C 642 MET cc_start: 0.8366 (mmm) cc_final: 0.8050 (mmt) REVERT: D 113 LYS cc_start: 0.9028 (mmmt) cc_final: 0.8527 (mmmt) REVERT: D 172 MET cc_start: 0.7558 (tpp) cc_final: 0.7017 (tpp) REVERT: D 264 LEU cc_start: 0.8662 (tt) cc_final: 0.8145 (tp) REVERT: D 377 MET cc_start: 0.8720 (ttp) cc_final: 0.8461 (ttp) outliers start: 35 outliers final: 22 residues processed: 186 average time/residue: 0.1313 time to fit residues: 40.8453 Evaluate side-chains 175 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 TYR Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 172 MET Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 531 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 167 optimal weight: 0.8980 chunk 217 optimal weight: 0.0050 chunk 11 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 205 optimal weight: 0.0670 chunk 194 optimal weight: 0.9980 chunk 111 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 90 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.5932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 263 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 = 0.3565 r_free = 0.3565 target = 0.067371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.051014 restraints weight = 83024.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.052726 restraints weight = 43164.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.052794 restraints weight = 29790.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.053666 restraints weight = 30043.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.053537 restraints weight = 27126.792| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 21010 Z= 0.102 Angle : 0.560 9.493 28490 Z= 0.266 Chirality : 0.041 0.313 3394 Planarity : 0.003 0.034 3532 Dihedral : 6.528 62.927 3306 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.28 % Allowed : 12.66 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.17), residues: 2528 helix: 2.53 (0.16), residues: 1060 sheet: -0.47 (0.27), residues: 358 loop : 0.43 (0.20), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 443 TYR 0.009 0.001 TYR A 81 PHE 0.021 0.001 PHE B 532 TRP 0.003 0.000 TRP B 183 HIS 0.002 0.001 HIS A 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.10 (20982) covalent geometry : angle 0.54595 / 0.26 (28414) SS BOND : bond 0.00163 / 0.10 ( 8) SS BOND : angle 0.38219 / 0.24 ( 16) hydrogen bonds : bond 0.03118 / 2.08 ( 1004) hydrogen bonds : angle 4.51067 / 3.28 ( 2934) link_BETA1-4 : bond 0.00443 / 0.29 ( 8) link_BETA1-4 : angle 3.27412 / 2.20 ( 24) link_NAG-ASN : bond 0.00392 / 0.27 ( 12) link_NAG-ASN : angle 2.37802 / 1.95 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 LEU cc_start: 0.9096 (mm) cc_final: 0.8881 (mt) REVERT: A 401 MET cc_start: 0.9221 (mmm) cc_final: 0.9012 (mmm) REVERT: A 642 MET cc_start: 0.8386 (mmm) cc_final: 0.8058 (mmt) REVERT: B 113 LYS cc_start: 0.8897 (mmmt) cc_final: 0.8639 (mmmt) REVERT: B 172 MET cc_start: 0.7753 (tpp) cc_final: 0.7257 (tpp) REVERT: B 207 MET cc_start: 0.9029 (mmp) cc_final: 0.8682 (mmp) REVERT: B 264 LEU cc_start: 0.8664 (tt) cc_final: 0.8161 (tp) REVERT: B 536 LYS cc_start: 0.8772 (ttpt) cc_final: 0.8203 (tptp) REVERT: C 171 PHE cc_start: 0.8551 (OUTLIER) cc_final: 0.8154 (m-80) REVERT: C 401 MET cc_start: 0.9225 (mmm) cc_final: 0.9002 (mmm) REVERT: C 642 MET cc_start: 0.8349 (mmm) cc_final: 0.8069 (mmt) REVERT: D 113 LYS cc_start: 0.9026 (mmmt) cc_final: 0.8533 (mmmt) REVERT: D 172 MET cc_start: 0.7637 (tpp) cc_final: 0.7070 (tpp) REVERT: D 264 LEU cc_start: 0.8655 (tt) cc_final: 0.8161 (tp) REVERT: D 377 MET cc_start: 0.8722 (ttp) cc_final: 0.8430 (ttp) outliers start: 29 outliers final: 16 residues processed: 185 average time/residue: 0.1376 time to fit residues: 42.3354 Evaluate side-chains 166 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 TYR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 351 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 22 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 175 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 0.9990 chunk 159 optimal weight: 3.9990 chunk 33 optimal weight: 0.0040 chunk 226 optimal weight: 0.0980 overall best weight: 0.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 606 ASN ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.066798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.049980 restraints weight = 83445.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.051915 restraints weight = 43138.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.053131 restraints weight = 29657.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.053912 restraints weight = 23816.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.054410 restraints weight = 20793.858| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21010 Z= 0.121 Angle : 0.576 10.419 28490 Z= 0.275 Chirality : 0.041 0.314 3394 Planarity : 0.003 0.035 3532 Dihedral : 6.477 61.612 3304 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.10 % Allowed : 13.32 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.17), residues: 2528 helix: 2.55 (0.16), residues: 1060 sheet: -0.43 (0.27), residues: 370 loop : 0.48 (0.20), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 215 TYR 0.032 0.001 TYR A 597 PHE 0.029 0.001 PHE B 532 TRP 0.004 0.000 TRP D 160 HIS 0.002 0.001 HIS B 593 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (20982) covalent geometry : angle 0.56321 / 0.27 (28414) SS BOND : bond 0.00458 / 0.38 ( 8) SS BOND : angle 0.40215 / 0.26 ( 16) hydrogen bonds : bond 0.03206 / 2.14 ( 1004) hydrogen bonds : angle 4.50485 / 3.28 ( 2934) link_BETA1-4 : bond 0.00437 / 0.29 ( 8) link_BETA1-4 : angle 3.19309 / 2.15 ( 24) link_NAG-ASN : bond 0.00322 / 0.23 ( 12) link_NAG-ASN : angle 2.34863 / 1.93 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 286 LEU cc_start: 0.9080 (mm) cc_final: 0.8864 (mt) REVERT: A 401 MET cc_start: 0.9242 (mmm) cc_final: 0.9025 (mmm) REVERT: A 412 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7290 (pp20) REVERT: A 413 ASP cc_start: 0.6975 (p0) cc_final: 0.6700 (p0) REVERT: A 514 MET cc_start: 0.8327 (tpp) cc_final: 0.8077 (tpp) REVERT: B 172 MET cc_start: 0.7735 (tpp) cc_final: 0.7199 (tpp) REVERT: B 207 MET cc_start: 0.9073 (mmp) cc_final: 0.8797 (mmp) REVERT: B 264 LEU cc_start: 0.8673 (tt) cc_final: 0.8170 (tp) REVERT: B 536 LYS cc_start: 0.8666 (ttpt) cc_final: 0.8101 (tptp) REVERT: C 171 PHE cc_start: 0.8547 (OUTLIER) cc_final: 0.8135 (m-80) REVERT: C 401 MET cc_start: 0.9258 (mmm) cc_final: 0.9035 (mmm) REVERT: C 510 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8392 (t0) REVERT: C 514 MET cc_start: 0.8225 (tpp) cc_final: 0.7982 (tpp) REVERT: D 113 LYS cc_start: 0.9043 (mmmt) cc_final: 0.8572 (mmmt) REVERT: D 172 MET cc_start: 0.7658 (tpp) cc_final: 0.7071 (tpp) REVERT: D 264 LEU cc_start: 0.8688 (tt) cc_final: 0.8217 (tp) outliers start: 25 outliers final: 17 residues processed: 176 average time/residue: 0.1314 time to fit residues: 38.9088 Evaluate side-chains 168 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 149 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 TYR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 351 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 48 optimal weight: 0.0980 chunk 240 optimal weight: 5.9990 chunk 92 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 114 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 234 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 225 optimal weight: 0.2980 chunk 212 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 360 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.067010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.050184 restraints weight = 83327.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.052116 restraints weight = 43223.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.053367 restraints weight = 29730.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.054140 restraints weight = 23772.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.054601 restraints weight = 20747.954| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21010 Z= 0.112 Angle : 0.576 10.783 28490 Z= 0.274 Chirality : 0.041 0.306 3394 Planarity : 0.003 0.035 3532 Dihedral : 6.465 61.938 3304 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.97 % Allowed : 13.50 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.78 (0.18), residues: 2528 helix: 2.57 (0.16), residues: 1060 sheet: -0.56 (0.26), residues: 382 loop : 0.56 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 599 TYR 0.023 0.001 TYR B 597 PHE 0.052 0.001 PHE C 444 TRP 0.005 0.000 TRP D 160 HIS 0.002 0.000 HIS A 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 (20982) covalent geometry : angle 0.56309 / 0.27 (28414) SS BOND : bond 0.00157 / 0.10 ( 8) SS BOND : angle 0.40687 / 0.26 ( 16) hydrogen bonds : bond 0.03137 / 2.10 ( 1004) hydrogen bonds : angle 4.47820 / 3.26 ( 2934) link_BETA1-4 : bond 0.00407 / 0.26 ( 8) link_BETA1-4 : angle 3.18862 / 2.15 ( 24) link_NAG-ASN : bond 0.00357 / 0.25 ( 12) link_NAG-ASN : angle 2.29968 / 1.90 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.826 Fit side-chains REVERT: A 282 PHE cc_start: 0.8501 (m-80) cc_final: 0.8274 (m-80) REVERT: A 286 LEU cc_start: 0.9064 (mm) cc_final: 0.8853 (mt) REVERT: A 401 MET cc_start: 0.9240 (mmm) cc_final: 0.9026 (mmm) REVERT: A 412 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7189 (pp20) REVERT: A 413 ASP cc_start: 0.6952 (p0) cc_final: 0.6622 (p0) REVERT: A 514 MET cc_start: 0.8355 (tpp) cc_final: 0.8106 (tpp) REVERT: A 642 MET cc_start: 0.8311 (mmm) cc_final: 0.7975 (mmt) REVERT: B 113 LYS cc_start: 0.9132 (mmmt) cc_final: 0.8527 (mmmt) REVERT: B 172 MET cc_start: 0.7749 (tpp) cc_final: 0.7204 (tpp) REVERT: B 264 LEU cc_start: 0.8656 (tt) cc_final: 0.8155 (tp) REVERT: B 536 LYS cc_start: 0.8663 (ttpt) cc_final: 0.8123 (tptp) REVERT: C 171 PHE cc_start: 0.8545 (OUTLIER) cc_final: 0.8161 (m-80) REVERT: C 282 PHE cc_start: 0.8472 (m-80) cc_final: 0.8268 (m-80) REVERT: C 401 MET cc_start: 0.9257 (mmm) cc_final: 0.9036 (mmm) REVERT: C 510 ASP cc_start: 0.8736 (OUTLIER) cc_final: 0.8428 (m-30) REVERT: C 514 MET cc_start: 0.8253 (tpp) cc_final: 0.8012 (tpp) REVERT: C 642 MET cc_start: 0.8312 (mmm) cc_final: 0.7965 (mmt) REVERT: D 113 LYS cc_start: 0.9063 (mmmt) cc_final: 0.8566 (mmmt) REVERT: D 172 MET cc_start: 0.7665 (tpp) cc_final: 0.7074 (tpp) REVERT: D 207 MET cc_start: 0.9034 (mmp) cc_final: 0.8741 (mmp) REVERT: D 264 LEU cc_start: 0.8692 (tt) cc_final: 0.8225 (tp) REVERT: D 532 PHE cc_start: 0.6871 (m-80) cc_final: 0.6221 (m-80) outliers start: 22 outliers final: 17 residues processed: 168 average time/residue: 0.1272 time to fit residues: 36.3573 Evaluate side-chains 164 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 145 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 TYR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 377 MET Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 351 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 143 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 184 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 174 optimal weight: 0.5980 chunk 191 optimal weight: 6.9990 chunk 212 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 606 ASN ** B 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 606 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.065849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.048583 restraints weight = 84011.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.050527 restraints weight = 43223.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.051779 restraints weight = 29749.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.052581 restraints weight = 23813.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.053069 restraints weight = 20734.686| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21010 Z= 0.149 Angle : 0.603 11.303 28490 Z= 0.288 Chirality : 0.042 0.320 3394 Planarity : 0.003 0.034 3532 Dihedral : 6.482 62.770 3304 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.01 % Allowed : 13.90 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.18), residues: 2528 helix: 2.54 (0.16), residues: 1060 sheet: -0.64 (0.26), residues: 392 loop : 0.54 (0.20), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 215 TYR 0.020 0.001 TYR B 597 PHE 0.049 0.001 PHE C 444 TRP 0.004 0.001 TRP D 160 HIS 0.002 0.001 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (20982) covalent geometry : angle 0.59121 / 0.29 (28414) SS BOND : bond 0.00203 / 0.13 ( 8) SS BOND : angle 0.37853 / 0.23 ( 16) hydrogen bonds : bond 0.03277 / 2.19 ( 1004) hydrogen bonds : angle 4.52182 / 3.28 ( 2934) link_BETA1-4 : bond 0.00358 / 0.22 ( 8) link_BETA1-4 : angle 3.09115 / 2.08 ( 24) link_NAG-ASN : bond 0.00286 / 0.20 ( 12) link_NAG-ASN : angle 2.34268 / 1.95 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5056 Ramachandran restraints generated. 2528 Oldfield, 0 Emsley, 2528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 282 PHE cc_start: 0.8575 (m-80) cc_final: 0.8326 (m-80) REVERT: A 286 LEU cc_start: 0.9094 (mm) cc_final: 0.8881 (mt) REVERT: A 401 MET cc_start: 0.9276 (mmm) cc_final: 0.9062 (mmm) REVERT: A 412 GLU cc_start: 0.7794 (tm-30) cc_final: 0.7226 (pp20) REVERT: A 413 ASP cc_start: 0.6975 (p0) cc_final: 0.6600 (p0) REVERT: A 514 MET cc_start: 0.8388 (tpp) cc_final: 0.8120 (tpp) REVERT: A 642 MET cc_start: 0.8401 (mmm) cc_final: 0.8035 (mmt) REVERT: B 113 LYS cc_start: 0.9151 (mmmt) cc_final: 0.8541 (mmmt) REVERT: B 172 MET cc_start: 0.7738 (tpp) cc_final: 0.7172 (tpp) REVERT: B 207 MET cc_start: 0.9073 (mmp) cc_final: 0.8766 (mmp) REVERT: B 264 LEU cc_start: 0.8660 (tt) cc_final: 0.8154 (tp) REVERT: C 171 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.8090 (m-80) REVERT: C 282 PHE cc_start: 0.8565 (m-80) cc_final: 0.8335 (m-80) REVERT: C 401 MET cc_start: 0.9283 (mmm) cc_final: 0.9071 (mmm) REVERT: C 514 MET cc_start: 0.8274 (tpp) cc_final: 0.8020 (tpp) REVERT: C 642 MET cc_start: 0.8414 (mmm) cc_final: 0.8032 (mmt) REVERT: D 113 LYS cc_start: 0.9097 (mmmt) cc_final: 0.8610 (mmmt) REVERT: D 172 MET cc_start: 0.7688 (tpp) cc_final: 0.7063 (tpp) REVERT: D 207 MET cc_start: 0.9084 (mmp) cc_final: 0.8801 (mmp) REVERT: D 264 LEU cc_start: 0.8708 (tt) cc_final: 0.8226 (tp) outliers start: 23 outliers final: 16 residues processed: 164 average time/residue: 0.1307 time to fit residues: 36.1972 Evaluate side-chains 160 residues out of total 2302 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 TYR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 222 THR Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain C residue 81 TYR Chi-restraints excluded: chain C residue 171 PHE Chi-restraints excluded: chain C residue 195 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 222 THR Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 351 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 239 optimal weight: 0.6980 chunk 168 optimal weight: 4.9990 chunk 201 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 76 optimal weight: 9.9990 chunk 231 optimal weight: 2.9990 chunk 82 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 263 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 = 0.3467 r_free = 0.3467 target = 0.064116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.046932 restraints weight = 83577.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.048783 restraints weight = 43532.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.049983 restraints weight = 30222.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.050761 restraints weight = 24332.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.051248 restraints weight = 21232.703| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 21010 Z= 0.234 Angle : 0.666 11.719 28490 Z= 0.322 Chirality : 0.044 0.383 3394 Planarity : 0.003 0.036 3532 Dihedral : 6.696 63.438 3304 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.84 % Allowed : 13.98 % Favored : 85.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.17), residues: 2528 helix: 2.32 (0.16), residues: 1064 sheet: -0.55 (0.26), residues: 378 loop : 0.40 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 215 TYR 0.020 0.001 TYR B 597 PHE 0.042 0.002 PHE C 444 TRP 0.008 0.001 TRP C 160 HIS 0.003 0.001 HIS A 555 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.23 (20982) covalent geometry : angle 0.65566 / 0.32 (28414) SS BOND : bond 0.00311 / 0.21 ( 8) SS BOND : angle 0.56894 / 0.33 ( 16) hydrogen bonds : bond 0.03754 / 2.54 ( 1004) hydrogen bonds : angle 4.69469 / 3.41 ( 2934) link_BETA1-4 : bond 0.00387 / 0.25 ( 8) link_BETA1-4 : angle 2.89325 / 1.95 ( 24) link_NAG-ASN : bond 0.00251 / 0.17 ( 12) link_NAG-ASN : angle 2.52413 / 2.13 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4121.83 seconds wall clock time: 71 minutes 50.39 seconds (4310.39 seconds total)