Starting phenix.real_space_refine on Fri Aug 7 11:09:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y9d_72694/08_2026/9y9d_72694.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y9d_72694/08_2026/9y9d_72694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y9d_72694/08_2026/9y9d_72694.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y9d_72694/08_2026/9y9d_72694.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y9d_72694/08_2026/9y9d_72694.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y9d_72694/08_2026/9y9d_72694.map" } resolution = 3.48 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: 7 Type Number sf(0) Gaussians P 12 5.49 5 Mg 16 5.21 5 S 112 5.16 5 Na 6 4.78 5 C 13194 2.51 5 N 3364 2.21 5 O 3954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 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: 20658 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5076 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: 5040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5040 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: 5076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5076 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: 5040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 637, 5040 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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 51 Unusual residues: {' MG': 4, ' NA': 2, 'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 50 Unusual residues: {' MG': 4, ' NA': 1, 'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 51 Unusual residues: {' MG': 4, ' NA': 2, 'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} 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: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 50 Unusual residues: {' MG': 4, ' NA': 1, 'ATP': 1, 'NAG': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.61, per 1000 atoms: 0.22 Number of scatterers: 20658 At special positions: 0 Unit cell: (124.267, 112.101, 227.678, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 112 16.00 P 12 15.00 Mg 16 11.99 Na 6 11.00 O 3954 8.00 N 3364 7.00 C 13194 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=2.02 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=2.02 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 908 " - " ASN A 127 " " NAG B 907 " - " ASN B 127 " " NAG C 908 " - " ASN C 127 " " NAG D 907 " - " 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: 1.50 Conformation dependent library (CDL) restraints added in 773.3 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: 110 helices and 36 sheets defined 48.7% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 82 through 86 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: 4.154A 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: 4.046A pdb=" N LYS A 238 " --> pdb=" O PRO A 234 " (cutoff:3.500A) removed outlier: 3.943A 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: 3.920A 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: 3.617A 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: 3.667A 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: 3.704A 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: 3.904A pdb=" N THR A 645 " --> pdb=" O THR A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 726 Processing helix chain 'B' and resid 82 through 86 Processing helix chain 'B' and resid 87 through 89 No H-bonds generated for 'chain 'B' and resid 87 through 89' Processing helix chain 'B' and resid 98 through 105 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: 4.071A 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: 4.100A 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: 4.046A pdb=" N ILE B 376 " --> pdb=" O THR B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 404 removed outlier: 3.676A 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: 3.768A 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 removed outlier: 3.575A pdb=" N ALA B 538 " --> pdb=" O ALA B 534 " (cutoff:3.500A) 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: 3.597A pdb=" N TYR B 601 " --> pdb=" O ALA B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 641 through 646 removed outlier: 4.453A 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 82 through 86 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: 4.154A 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: 4.046A pdb=" N LYS C 238 " --> pdb=" O PRO C 234 " (cutoff:3.500A) removed outlier: 3.944A 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: 3.920A 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: 3.616A 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: 3.667A 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: 3.703A 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: 3.904A pdb=" N THR C 645 " --> pdb=" O THR C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 713 through 726 Processing helix chain 'D' and resid 82 through 86 Processing helix chain 'D' and resid 87 through 89 No H-bonds generated for 'chain 'D' and resid 87 through 89' Processing helix chain 'D' and resid 98 through 105 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: 4.071A 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: 4.100A 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: 4.047A pdb=" N ILE D 376 " --> pdb=" O THR D 372 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 404 removed outlier: 3.675A 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: 3.769A 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 removed outlier: 3.575A pdb=" N ALA D 538 " --> pdb=" O ALA D 534 " (cutoff:3.500A) 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: 4.453A pdb=" N THR D 645 " --> pdb=" O THR D 641 " (cutoff:3.500A) removed outlier: 4.113A 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: 6.731A pdb=" N TYR A 79 " --> pdb=" O VAL A 47 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N MET A 49 " --> pdb=" O ARG A 77 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG A 77 " --> pdb=" O MET A 49 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N LEU A 51 " --> pdb=" O ASN A 75 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASN A 75 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER A 53 " --> pdb=" O THR A 73 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N THR A 73 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER A 129 " --> pdb=" O ASN A 122 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASN A 122 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL A 131 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU A 120 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.708A 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: 6.522A pdb=" N ILE A 66 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL A 173 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.085A 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: 6.522A pdb=" N ILE A 66 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL A 173 " --> pdb=" O ILE A 66 " (cutoff:3.500A) removed outlier: 6.085A 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: 3.849A pdb=" N PHE A 487 " --> pdb=" O ASN A 479 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL A 475 " --> pdb=" O LEU A 491 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU A 493 " --> pdb=" O ALA A 473 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ALA A 473 " --> pdb=" O LEU A 493 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N HIS A 450 " --> pdb=" O ILE A 474 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLN A 476 " --> pdb=" O HIS A 450 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL A 452 " --> pdb=" O GLN A 476 " (cutoff:3.500A) removed outlier: 7.881A 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: 4.228A 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: 6.402A pdb=" N GLN A 707 " --> pdb=" O LEU A 616 " (cutoff:3.500A) removed outlier: 3.871A 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: 3.939A 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: 5.303A pdb=" N ILE B 46 " --> pdb=" O TYR B 81 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TYR B 81 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B 48 " --> pdb=" O TYR B 79 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN B 75 " --> pdb=" O ALA B 52 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N CYS B 54 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR B 73 " --> pdb=" O CYS B 54 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER B 129 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL B 123 " --> pdb=" O SER B 129 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN B 119 " --> pdb=" O VAL B 133 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU B 135 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 5.925A 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: 6.518A pdb=" N ILE B 66 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL B 173 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.300A 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: 6.518A pdb=" N ILE B 66 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL B 173 " --> pdb=" O ILE B 66 " (cutoff:3.500A) removed outlier: 6.300A 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: 6.688A pdb=" N VAL B 475 " --> pdb=" O LEU B 491 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU B 493 " --> pdb=" O ALA B 473 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA B 473 " --> pdb=" O LEU B 493 " (cutoff:3.500A) removed outlier: 4.380A 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: 6.256A pdb=" N ILE B 408 " --> pdb=" O ILE B 421 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N ILE B 421 " --> pdb=" O ILE B 408 " (cutoff:3.500A) removed outlier: 6.660A 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: 3.903A 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: 6.490A 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: 3.864A 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: 6.732A pdb=" N TYR C 79 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N MET C 49 " --> pdb=" O ARG C 77 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ARG C 77 " --> pdb=" O MET C 49 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N LEU C 51 " --> pdb=" O ASN C 75 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N ASN C 75 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER C 53 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N THR C 73 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N SER C 129 " --> pdb=" O ASN C 122 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN C 122 " --> pdb=" O SER C 129 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N VAL C 131 " --> pdb=" O LEU C 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU C 120 " --> pdb=" O VAL C 131 " (cutoff:3.500A) removed outlier: 6.707A 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: 6.522A pdb=" N ILE C 66 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL C 173 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 6.087A 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: 6.522A pdb=" N ILE C 66 " --> pdb=" O PHE C 171 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N VAL C 173 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 6.087A 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: 3.849A pdb=" N PHE C 487 " --> pdb=" O ASN C 479 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL C 475 " --> pdb=" O LEU C 491 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LEU C 493 " --> pdb=" O ALA C 473 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ALA C 473 " --> pdb=" O LEU C 493 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N HIS C 450 " --> pdb=" O ILE C 474 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLN C 476 " --> pdb=" O HIS C 450 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL C 452 " --> pdb=" O GLN C 476 " (cutoff:3.500A) removed outlier: 7.882A 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: 4.228A 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: 6.402A pdb=" N GLN C 707 " --> pdb=" O LEU C 616 " (cutoff:3.500A) removed outlier: 3.871A 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: 3.940A 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: 5.304A pdb=" N ILE D 46 " --> pdb=" O TYR D 81 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N TYR D 81 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY D 48 " --> pdb=" O TYR D 79 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN D 75 " --> pdb=" O ALA D 52 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N CYS D 54 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR D 73 " --> pdb=" O CYS D 54 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N SER D 129 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N VAL D 123 " --> pdb=" O SER D 129 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN D 119 " --> pdb=" O VAL D 133 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N LEU D 135 " --> pdb=" O VAL D 117 " (cutoff:3.500A) removed outlier: 5.925A 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: 6.518A pdb=" N ILE D 66 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL D 173 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 6.300A 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: 6.518A pdb=" N ILE D 66 " --> pdb=" O PHE D 171 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N VAL D 173 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 6.300A 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: 3.669A pdb=" N PHE D 487 " --> pdb=" O ASN D 479 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL D 475 " --> pdb=" O LEU D 491 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU D 493 " --> pdb=" O ALA D 473 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA D 473 " --> pdb=" O LEU D 493 " (cutoff:3.500A) removed outlier: 4.381A 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: 6.256A pdb=" N ILE D 408 " --> pdb=" O ILE D 421 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N ILE D 421 " --> pdb=" O ILE D 408 " (cutoff:3.500A) removed outlier: 6.659A 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: 3.903A 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: 6.490A 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: 3.864A 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 1036 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: 3.13 Time building geometry restraints manager: 2.04 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: 6535 1.34 - 1.46: 3340 1.46 - 1.57: 10915 1.57 - 1.69: 20 1.69 - 1.81: 188 Bond restraints: 20998 Sorted by residual: bond pdb=" N VAL C 96 " pdb=" CA VAL C 96 " ideal model delta sigma weight residual 1.458 1.495 -0.038 1.14e-02 7.69e+03 1.08e+01 bond pdb=" N VAL A 96 " pdb=" CA VAL A 96 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.14e-02 7.69e+03 1.04e+01 bond pdb=" N ASP D 98 " pdb=" CA ASP D 98 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.43e+00 bond pdb=" N ASP B 98 " pdb=" CA ASP B 98 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.25e-02 6.40e+03 8.43e+00 bond pdb=" N GLU A 349 " pdb=" CA GLU A 349 " ideal model delta sigma weight residual 1.462 1.489 -0.027 9.50e-03 1.11e+04 8.24e+00 ... (remaining 20993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 27150 1.08 - 2.16: 965 2.16 - 3.24: 224 3.24 - 4.32: 63 4.32 - 5.40: 32 Bond angle restraints: 28434 Sorted by residual: angle pdb=" CA ASP D 98 " pdb=" CB ASP D 98 " pdb=" CG ASP D 98 " ideal model delta sigma weight residual 112.60 115.89 -3.29 1.00e+00 1.00e+00 1.08e+01 angle pdb=" CA ASP B 98 " pdb=" CB ASP B 98 " pdb=" CG ASP B 98 " ideal model delta sigma weight residual 112.60 115.86 -3.26 1.00e+00 1.00e+00 1.06e+01 angle pdb=" CA THR A 101 " pdb=" CB THR A 101 " pdb=" OG1 THR A 101 " ideal model delta sigma weight residual 109.60 104.97 4.63 1.50e+00 4.44e-01 9.53e+00 angle pdb=" CA ASP B 98 " pdb=" C ASP B 98 " pdb=" O ASP B 98 " ideal model delta sigma weight residual 121.45 118.16 3.29 1.07e+00 8.73e-01 9.46e+00 angle pdb=" C GLU A 349 " pdb=" N PRO A 350 " pdb=" CA PRO A 350 " ideal model delta sigma weight residual 119.05 122.46 -3.41 1.11e+00 8.12e-01 9.41e+00 ... (remaining 28429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.18: 11872 12.18 - 24.36: 930 24.36 - 36.54: 178 36.54 - 48.72: 82 48.72 - 60.90: 36 Dihedral angle restraints: 13098 sinusoidal: 5630 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 180.00 163.54 16.46 0 5.00e+00 4.00e-02 1.08e+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 180.00 163.54 16.46 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA CYS A 291 " pdb=" C CYS A 291 " pdb=" N SER A 292 " pdb=" CA SER A 292 " ideal model delta harmonic sigma weight residual 180.00 164.19 15.81 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 13095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 3232 0.098 - 0.196: 156 0.196 - 0.294: 2 0.294 - 0.391: 0 0.391 - 0.489: 4 Chirality restraints: 3394 Sorted by residual: 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 -2.23 -0.17 2.00e-02 2.50e+03 7.50e+01 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 -2.23 -0.17 2.00e-02 2.50e+03 7.45e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.30 -0.10 2.00e-02 2.50e+03 2.31e+01 ... (remaining 3391 not shown) Planarity restraints: 3548 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 431 " -0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO A 432 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 432 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 432 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE D 408 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO D 409 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO D 409 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 409 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 431 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO C 432 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO C 432 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 432 " -0.017 5.00e-02 4.00e+02 ... (remaining 3545 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 291 2.70 - 3.25: 20480 3.25 - 3.80: 31620 3.80 - 4.35: 41799 4.35 - 4.90: 71049 Nonbonded interactions: 165239 Sorted by model distance: nonbonded pdb=" OD2 ASP C 510 " pdb="MG MG C 902 " model vdw 2.154 2.170 nonbonded pdb=" OD2 ASP A 510 " pdb="MG MG A 902 " model vdw 2.154 2.170 nonbonded pdb=" CG ASP C 510 " pdb="MG MG C 902 " model vdw 2.169 2.400 nonbonded pdb=" CG ASP A 510 " pdb="MG MG A 902 " model vdw 2.169 2.400 nonbonded pdb=" O ILE D 508 " pdb="MG MG D 903 " model vdw 2.320 2.170 ... (remaining 165234 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: 0.03 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.770 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: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 17.330 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6979 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 : 0.004 0.043 21026 Z= 0.211 Angle : 0.572 10.009 28510 Z= 0.301 Chirality : 0.046 0.489 3394 Planarity : 0.003 0.032 3536 Dihedral : 10.098 60.898 8238 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.05 % Allowed : 4.39 % Favored : 94.56 % 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: 0.65 (0.17), residues: 2528 helix: 1.74 (0.16), residues: 1020 sheet: -1.00 (0.24), residues: 438 loop : -0.11 (0.20), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 713 TYR 0.011 0.001 TYR C 638 PHE 0.016 0.001 PHE D 67 TRP 0.005 0.001 TRP D 163 HIS 0.004 0.001 HIS C 185 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 (20998) covalent geometry : angle 0.54232 / 0.29 (28434) SS BOND : bond 0.00456 / 0.29 ( 8) SS BOND : angle 0.37610 / 0.24 ( 16) hydrogen bonds : bond 0.11376 / 7.43 ( 1012) hydrogen bonds : angle 6.49369 / 4.64 ( 2934) link_BETA1-4 : bond 0.00259 / 0.18 ( 8) link_BETA1-4 : angle 4.98431 / 3.44 ( 24) link_NAG-ASN : bond 0.00476 / 0.34 ( 12) link_NAG-ASN : angle 3.22557 / 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 280 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 256 time to evaluate : 0.667 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 532 PHE cc_start: 0.4674 (m-80) cc_final: 0.4376 (m-10) outliers start: 24 outliers final: 6 residues processed: 278 average time/residue: 0.1542 time to fit residues: 63.5055 Evaluate side-chains 150 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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: 0.0970 chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 0.4980 chunk 227 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 247 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 254 ASN A 337 ASN A 600 HIS B 185 HIS B 254 ASN B 263 ASN B 528 ASN B 540 ASN C 254 ASN C 337 ASN C 600 HIS D 185 HIS D 254 ASN D 263 ASN D 528 ASN D 540 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.056438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.041937 restraints weight = 99020.923| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 4.58 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21026 Z= 0.131 Angle : 0.592 8.442 28510 Z= 0.292 Chirality : 0.042 0.340 3394 Planarity : 0.003 0.026 3536 Dihedral : 6.897 60.186 3308 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.14 % Allowed : 8.52 % Favored : 90.34 % 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: 1.06 (0.17), residues: 2528 helix: 2.13 (0.16), residues: 1006 sheet: -0.67 (0.25), residues: 430 loop : 0.01 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 724 TYR 0.008 0.001 TYR D 597 PHE 0.013 0.001 PHE C 612 TRP 0.005 0.001 TRP D 163 HIS 0.006 0.001 HIS D 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (20998) covalent geometry : angle 0.57383 / 0.29 (28434) SS BOND : bond 0.00252 / 0.16 ( 8) SS BOND : angle 0.32591 / 0.21 ( 16) hydrogen bonds : bond 0.03744 / 2.54 ( 1012) hydrogen bonds : angle 5.10699 / 3.63 ( 2934) link_BETA1-4 : bond 0.00447 / 0.30 ( 8) link_BETA1-4 : angle 3.65712 / 2.50 ( 24) link_NAG-ASN : bond 0.00415 / 0.29 ( 12) link_NAG-ASN : angle 2.92588 / 2.35 ( 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 178 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.514 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: B 49 MET cc_start: 0.8961 (ptm) cc_final: 0.8683 (ppp) REVERT: B 377 MET cc_start: 0.8634 (ttp) cc_final: 0.8275 (ttp) REVERT: B 402 GLU cc_start: 0.9269 (tt0) cc_final: 0.8998 (tp30) REVERT: B 532 PHE cc_start: 0.7992 (m-80) cc_final: 0.6995 (m-10) REVERT: D 49 MET cc_start: 0.8949 (ptm) cc_final: 0.8666 (ppp) REVERT: D 377 MET cc_start: 0.8636 (ttp) cc_final: 0.8273 (ttp) REVERT: D 402 GLU cc_start: 0.9282 (tt0) cc_final: 0.9010 (tp30) REVERT: D 532 PHE cc_start: 0.7963 (m-10) cc_final: 0.6934 (m-10) outliers start: 26 outliers final: 14 residues processed: 176 average time/residue: 0.1274 time to fit residues: 35.4790 Evaluate side-chains 146 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 316 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 413 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 237 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 23 optimal weight: 0.0770 chunk 203 optimal weight: 4.9990 chunk 137 optimal weight: 0.8980 chunk 159 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 208 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 540 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 = 0.3438 r_free = 0.3438 target = 0.056092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.042453 restraints weight = 99975.003| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 4.60 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21026 Z= 0.117 Angle : 0.557 7.865 28510 Z= 0.274 Chirality : 0.041 0.330 3394 Planarity : 0.003 0.026 3536 Dihedral : 6.732 61.234 3308 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.27 % Allowed : 9.00 % Favored : 89.73 % 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: 1.30 (0.17), residues: 2528 helix: 2.25 (0.16), residues: 1028 sheet: -0.46 (0.25), residues: 420 loop : 0.14 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 333 TYR 0.016 0.001 TYR D 597 PHE 0.013 0.001 PHE A 612 TRP 0.004 0.000 TRP D 163 HIS 0.005 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (20998) covalent geometry : angle 0.53873 / 0.27 (28434) SS BOND : bond 0.00209 / 0.14 ( 8) SS BOND : angle 0.33756 / 0.21 ( 16) hydrogen bonds : bond 0.03443 / 2.34 ( 1012) hydrogen bonds : angle 4.83918 / 3.44 ( 2934) link_BETA1-4 : bond 0.00455 / 0.28 ( 8) link_BETA1-4 : angle 3.57301 / 2.43 ( 24) link_NAG-ASN : bond 0.00396 / 0.27 ( 12) link_NAG-ASN : angle 2.76761 / 2.23 ( 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 164 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 135 time to evaluate : 0.851 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: A 344 MET cc_start: 0.9619 (tmm) cc_final: 0.9277 (tmm) REVERT: B 49 MET cc_start: 0.8937 (ptm) cc_final: 0.8686 (ppp) REVERT: B 248 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9038 (mp) REVERT: B 377 MET cc_start: 0.8567 (ttp) cc_final: 0.8232 (ttt) REVERT: C 185 HIS cc_start: 0.7591 (OUTLIER) cc_final: 0.7388 (t70) REVERT: C 344 MET cc_start: 0.9625 (tmm) cc_final: 0.9290 (tmm) REVERT: D 49 MET cc_start: 0.8951 (ptm) cc_final: 0.8670 (ppp) REVERT: D 248 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9042 (mp) REVERT: D 377 MET cc_start: 0.8580 (ttp) cc_final: 0.8243 (ttt) outliers start: 29 outliers final: 18 residues processed: 159 average time/residue: 0.1266 time to fit residues: 32.8492 Evaluate side-chains 145 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 435 CYS Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 185 HIS Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 435 CYS Chi-restraints excluded: chain D residue 578 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 110 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 63 optimal weight: 10.0000 chunk 15 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 chunk 84 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 188 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 540 ASN ** D 540 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.055412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.040925 restraints weight = 100721.600| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 4.63 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 21026 Z= 0.125 Angle : 0.535 7.802 28510 Z= 0.263 Chirality : 0.041 0.325 3394 Planarity : 0.003 0.028 3536 Dihedral : 6.634 63.009 3308 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.36 % Allowed : 9.17 % Favored : 89.46 % 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: 1.45 (0.17), residues: 2528 helix: 2.37 (0.17), residues: 1036 sheet: -0.42 (0.25), residues: 420 loop : 0.23 (0.20), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 577 TYR 0.014 0.001 TYR B 515 PHE 0.014 0.001 PHE D 532 TRP 0.003 0.001 TRP D 163 HIS 0.005 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.13 (20998) covalent geometry : angle 0.51822 / 0.26 (28434) SS BOND : bond 0.00203 / 0.13 ( 8) SS BOND : angle 0.34798 / 0.23 ( 16) hydrogen bonds : bond 0.03313 / 2.25 ( 1012) hydrogen bonds : angle 4.65605 / 3.31 ( 2934) link_BETA1-4 : bond 0.00318 / 0.23 ( 8) link_BETA1-4 : angle 3.43318 / 2.32 ( 24) link_NAG-ASN : bond 0.00354 / 0.24 ( 12) link_NAG-ASN : angle 2.64370 / 2.14 ( 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 162 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 0.754 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: A 344 MET cc_start: 0.9632 (tmm) cc_final: 0.9430 (tmm) REVERT: B 49 MET cc_start: 0.8998 (ptm) cc_final: 0.8755 (ppp) REVERT: B 248 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9017 (mp) REVERT: B 377 MET cc_start: 0.8620 (ttp) cc_final: 0.8322 (ttp) REVERT: C 344 MET cc_start: 0.9630 (tmm) cc_final: 0.9428 (tmm) REVERT: D 49 MET cc_start: 0.9015 (ptm) cc_final: 0.8758 (ppp) REVERT: D 248 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8992 (mp) REVERT: D 377 MET cc_start: 0.8607 (ttp) cc_final: 0.8295 (ttp) outliers start: 31 outliers final: 16 residues processed: 159 average time/residue: 0.1289 time to fit residues: 33.3971 Evaluate side-chains 143 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 578 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 74 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 chunk 193 optimal weight: 20.0000 chunk 223 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 218 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 212 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 89 optimal weight: 0.8980 chunk 109 optimal weight: 0.0980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 540 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.055578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.041192 restraints weight = 99256.466| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 4.53 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21026 Z= 0.107 Angle : 0.527 7.804 28510 Z= 0.260 Chirality : 0.041 0.318 3394 Planarity : 0.003 0.028 3536 Dihedral : 6.580 64.770 3308 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 1.58 % Allowed : 9.09 % Favored : 89.33 % 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: 1.56 (0.18), residues: 2528 helix: 2.40 (0.17), residues: 1046 sheet: -0.36 (0.25), residues: 420 loop : 0.35 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 577 TYR 0.009 0.001 TYR B 597 PHE 0.014 0.001 PHE B 532 TRP 0.003 0.000 TRP D 163 HIS 0.005 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.11 (20998) covalent geometry : angle 0.51095 / 0.26 (28434) SS BOND : bond 0.00173 / 0.11 ( 8) SS BOND : angle 0.34118 / 0.22 ( 16) hydrogen bonds : bond 0.03143 / 2.14 ( 1012) hydrogen bonds : angle 4.54244 / 3.23 ( 2934) link_BETA1-4 : bond 0.00370 / 0.24 ( 8) link_BETA1-4 : angle 3.39914 / 2.28 ( 24) link_NAG-ASN : bond 0.00379 / 0.25 ( 12) link_NAG-ASN : angle 2.53098 / 2.06 ( 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 160 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 124 time to evaluate : 0.641 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: A 174 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8570 (pt0) REVERT: B 248 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9008 (mp) REVERT: B 377 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8300 (ttt) REVERT: D 49 MET cc_start: 0.9001 (ptm) cc_final: 0.8784 (ppp) REVERT: D 172 MET cc_start: 0.7771 (ttp) cc_final: 0.7106 (ttt) REVERT: D 248 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9012 (mp) REVERT: D 377 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8317 (ttt) outliers start: 36 outliers final: 18 residues processed: 151 average time/residue: 0.1205 time to fit residues: 29.9927 Evaluate side-chains 146 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 123 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain B residue 602 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain D residue 123 VAL Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 578 LEU Chi-restraints excluded: chain D residue 602 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 89 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 131 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 168 optimal weight: 0.2980 chunk 227 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 251 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.055664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.041224 restraints weight = 99681.412| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 4.52 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21026 Z= 0.100 Angle : 0.528 8.612 28510 Z= 0.258 Chirality : 0.041 0.314 3394 Planarity : 0.003 0.029 3536 Dihedral : 6.545 65.742 3306 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.23 % Allowed : 9.66 % Favored : 89.11 % 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: 1.59 (0.18), residues: 2528 helix: 2.37 (0.17), residues: 1044 sheet: -0.31 (0.25), residues: 420 loop : 0.41 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 338 TYR 0.006 0.001 TYR B 597 PHE 0.021 0.001 PHE D 532 TRP 0.003 0.000 TRP B 163 HIS 0.005 0.001 HIS D 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.10 (20998) covalent geometry : angle 0.51203 / 0.25 (28434) SS BOND : bond 0.00158 / 0.10 ( 8) SS BOND : angle 0.32670 / 0.21 ( 16) hydrogen bonds : bond 0.03051 / 2.08 ( 1012) hydrogen bonds : angle 4.48356 / 3.19 ( 2934) link_BETA1-4 : bond 0.00386 / 0.25 ( 8) link_BETA1-4 : angle 3.38370 / 2.27 ( 24) link_NAG-ASN : bond 0.00384 / 0.26 ( 12) link_NAG-ASN : angle 2.47122 / 2.01 ( 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 153 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.792 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: A 174 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8569 (pt0) REVERT: B 248 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8999 (mp) REVERT: B 377 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8269 (ttt) REVERT: D 248 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9006 (mp) REVERT: D 377 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.8284 (ttt) outliers start: 28 outliers final: 12 residues processed: 146 average time/residue: 0.1406 time to fit residues: 33.4423 Evaluate side-chains 142 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 125 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 578 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 100 optimal weight: 0.0170 chunk 109 optimal weight: 8.9990 chunk 241 optimal weight: 0.7980 chunk 49 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 131 optimal weight: 7.9990 chunk 182 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 223 optimal weight: 6.9990 overall best weight: 1.1022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.055143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.040864 restraints weight = 99594.845| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 4.47 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21026 Z= 0.112 Angle : 0.539 8.241 28510 Z= 0.262 Chirality : 0.041 0.313 3394 Planarity : 0.003 0.031 3536 Dihedral : 6.506 66.712 3304 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.32 % Allowed : 9.75 % Favored : 88.94 % 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: 1.62 (0.18), residues: 2528 helix: 2.38 (0.17), residues: 1044 sheet: -0.30 (0.24), residues: 420 loop : 0.45 (0.20), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 577 TYR 0.014 0.001 TYR C 597 PHE 0.034 0.001 PHE A 309 TRP 0.003 0.000 TRP B 163 HIS 0.005 0.001 HIS D 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (20998) covalent geometry : angle 0.52365 / 0.26 (28434) SS BOND : bond 0.00173 / 0.11 ( 8) SS BOND : angle 0.31626 / 0.21 ( 16) hydrogen bonds : bond 0.03058 / 2.09 ( 1012) hydrogen bonds : angle 4.45542 / 3.17 ( 2934) link_BETA1-4 : bond 0.00369 / 0.24 ( 8) link_BETA1-4 : angle 3.35225 / 2.24 ( 24) link_NAG-ASN : bond 0.00346 / 0.23 ( 12) link_NAG-ASN : angle 2.43149 / 1.99 ( 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 156 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 126 time to evaluate : 0.826 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: A 174 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8577 (pt0) REVERT: A 510 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.8636 (t0) REVERT: B 172 MET cc_start: 0.7829 (ttp) cc_final: 0.7309 (ttm) REVERT: B 248 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8999 (mp) REVERT: B 377 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.8285 (ttt) REVERT: C 510 ASP cc_start: 0.8830 (OUTLIER) cc_final: 0.8608 (t0) REVERT: D 248 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.9004 (mp) REVERT: D 377 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8269 (ttt) outliers start: 30 outliers final: 14 residues processed: 149 average time/residue: 0.1299 time to fit residues: 31.6855 Evaluate side-chains 142 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 510 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 578 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 214 optimal weight: 6.9990 chunk 74 optimal weight: 0.0970 chunk 215 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 241 optimal weight: 0.5980 chunk 14 optimal weight: 4.9990 chunk 198 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 196 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.055496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.041868 restraints weight = 99973.050| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 4.93 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21026 Z= 0.098 Angle : 0.533 8.070 28510 Z= 0.259 Chirality : 0.041 0.306 3394 Planarity : 0.003 0.032 3536 Dihedral : 6.498 69.006 3304 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.88 % Allowed : 10.45 % Favored : 88.67 % 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: 1.68 (0.18), residues: 2528 helix: 2.39 (0.17), residues: 1044 sheet: -0.26 (0.25), residues: 420 loop : 0.53 (0.21), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 599 TYR 0.035 0.001 TYR B 597 PHE 0.027 0.001 PHE C 309 TRP 0.002 0.000 TRP B 163 HIS 0.005 0.000 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (20998) covalent geometry : angle 0.51825 / 0.26 (28434) SS BOND : bond 0.00149 / 0.10 ( 8) SS BOND : angle 0.32813 / 0.21 ( 16) hydrogen bonds : bond 0.02965 / 2.03 ( 1012) hydrogen bonds : angle 4.40200 / 3.13 ( 2934) link_BETA1-4 : bond 0.00377 / 0.25 ( 8) link_BETA1-4 : angle 3.35232 / 2.23 ( 24) link_NAG-ASN : bond 0.00378 / 0.25 ( 12) link_NAG-ASN : angle 2.34982 / 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 145 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.658 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 174 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8551 (pt0) REVERT: A 377 MET cc_start: 0.8028 (ppp) cc_final: 0.7623 (ppp) REVERT: B 172 MET cc_start: 0.7903 (ttp) cc_final: 0.7391 (ttm) REVERT: B 248 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9033 (mp) REVERT: B 377 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8298 (ttt) REVERT: D 172 MET cc_start: 0.7853 (ttp) cc_final: 0.7382 (ttm) REVERT: D 248 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9032 (mp) REVERT: D 377 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8312 (ttt) outliers start: 20 outliers final: 9 residues processed: 139 average time/residue: 0.1298 time to fit residues: 29.5042 Evaluate side-chains 134 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 377 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 156 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 198 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 102 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.055266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.040883 restraints weight = 100012.080| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 4.52 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 21026 Z= 0.101 Angle : 0.541 9.327 28510 Z= 0.261 Chirality : 0.041 0.308 3394 Planarity : 0.003 0.032 3536 Dihedral : 6.492 70.573 3304 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.92 % Allowed : 10.97 % Favored : 88.10 % 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: 2.42 (0.17), residues: 1044 sheet: -0.25 (0.25), residues: 420 loop : 0.55 (0.21), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 77 TYR 0.027 0.001 TYR B 597 PHE 0.035 0.001 PHE D 532 TRP 0.002 0.000 TRP B 163 HIS 0.005 0.001 HIS B 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.10 (20998) covalent geometry : angle 0.52655 / 0.26 (28434) SS BOND : bond 0.00160 / 0.10 ( 8) SS BOND : angle 0.29252 / 0.19 ( 16) hydrogen bonds : bond 0.02943 / 2.02 ( 1012) hydrogen bonds : angle 4.39692 / 3.13 ( 2934) link_BETA1-4 : bond 0.00364 / 0.23 ( 8) link_BETA1-4 : angle 3.30963 / 2.20 ( 24) link_NAG-ASN : bond 0.00354 / 0.24 ( 12) link_NAG-ASN : angle 2.31775 / 1.91 ( 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 143 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.901 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 174 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8573 (pt0) REVERT: A 377 MET cc_start: 0.8063 (ppp) cc_final: 0.7608 (ppp) REVERT: A 597 TYR cc_start: 0.8284 (t80) cc_final: 0.8028 (t80) REVERT: B 172 MET cc_start: 0.7849 (ttp) cc_final: 0.7363 (ttm) REVERT: B 248 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.8995 (mp) REVERT: B 377 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8310 (ttt) REVERT: C 377 MET cc_start: 0.7953 (ppp) cc_final: 0.7543 (ppp) REVERT: C 597 TYR cc_start: 0.8314 (t80) cc_final: 0.8042 (t80) REVERT: D 172 MET cc_start: 0.7881 (ttp) cc_final: 0.7365 (ttm) REVERT: D 248 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8986 (mp) REVERT: D 377 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8293 (ttt) outliers start: 21 outliers final: 13 residues processed: 137 average time/residue: 0.1451 time to fit residues: 32.2511 Evaluate side-chains 137 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain A residue 513 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain C residue 513 ASP Chi-restraints excluded: chain D residue 248 LEU Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 377 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 187 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 134 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 201 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 174 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 727 ASN C 727 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.052742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.038347 restraints weight = 101604.727| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 4.51 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 21026 Z= 0.237 Angle : 0.661 9.311 28510 Z= 0.317 Chirality : 0.043 0.357 3394 Planarity : 0.003 0.039 3536 Dihedral : 6.712 75.917 3304 Min Nonbonded Distance : 1.812 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.05 % Allowed : 11.11 % Favored : 87.84 % 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: 1.49 (0.18), residues: 2528 helix: 2.25 (0.17), residues: 1042 sheet: -0.45 (0.24), residues: 440 loop : 0.48 (0.21), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 230 TYR 0.021 0.001 TYR A 597 PHE 0.034 0.002 PHE D 532 TRP 0.012 0.002 TRP A 160 HIS 0.005 0.001 HIS D 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.24 (20998) covalent geometry : angle 0.64999 / 0.31 (28434) SS BOND : bond 0.00397 / 0.26 ( 8) SS BOND : angle 0.71485 / 0.45 ( 16) hydrogen bonds : bond 0.03759 / 2.57 ( 1012) hydrogen bonds : angle 4.67259 / 3.32 ( 2934) link_BETA1-4 : bond 0.00227 / 0.17 ( 8) link_BETA1-4 : angle 3.13260 / 2.07 ( 24) link_NAG-ASN : bond 0.00398 / 0.26 ( 12) link_NAG-ASN : angle 2.46406 / 2.06 ( 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 146 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.742 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 174 GLU cc_start: 0.8778 (OUTLIER) cc_final: 0.8568 (pt0) REVERT: B 172 MET cc_start: 0.7990 (ttp) cc_final: 0.7484 (ttm) REVERT: B 377 MET cc_start: 0.8661 (OUTLIER) cc_final: 0.8303 (ttp) REVERT: D 172 MET cc_start: 0.7962 (ttp) cc_final: 0.7442 (ttm) REVERT: D 377 MET cc_start: 0.8664 (OUTLIER) cc_final: 0.8306 (ttp) outliers start: 24 outliers final: 15 residues processed: 140 average time/residue: 0.1205 time to fit residues: 27.4500 Evaluate side-chains 139 residues out of total 2306 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 202 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 309 PHE Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 377 MET Chi-restraints excluded: chain B residue 413 ASP Chi-restraints excluded: chain B residue 578 LEU Chi-restraints excluded: chain C residue 123 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 309 PHE Chi-restraints excluded: chain D residue 351 TYR Chi-restraints excluded: chain D residue 377 MET Chi-restraints excluded: chain D residue 413 ASP Chi-restraints excluded: chain D residue 578 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 94 optimal weight: 2.9990 chunk 189 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 171 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 60 optimal weight: 9.9990 chunk 134 optimal weight: 0.4980 chunk 65 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 177 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.054178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.039841 restraints weight = 100133.941| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 4.53 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21026 Z= 0.108 Angle : 0.573 9.592 28510 Z= 0.275 Chirality : 0.041 0.302 3394 Planarity : 0.003 0.034 3536 Dihedral : 6.656 80.163 3304 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 0.92 % Allowed : 11.33 % Favored : 87.75 % 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: 1.64 (0.18), residues: 2528 helix: 2.33 (0.17), residues: 1048 sheet: -0.38 (0.24), residues: 434 loop : 0.61 (0.21), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 77 TYR 0.024 0.001 TYR D 597 PHE 0.035 0.001 PHE D 532 TRP 0.003 0.000 TRP D 163 HIS 0.006 0.001 HIS D 103 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (20998) covalent geometry : angle 0.56026 / 0.27 (28434) SS BOND : bond 0.00211 / 0.14 ( 8) SS BOND : angle 0.41748 / 0.27 ( 16) hydrogen bonds : bond 0.03144 / 2.15 ( 1012) hydrogen bonds : angle 4.47327 / 3.18 ( 2934) link_BETA1-4 : bond 0.00395 / 0.24 ( 8) link_BETA1-4 : angle 3.27593 / 2.16 ( 24) link_NAG-ASN : bond 0.00357 / 0.24 ( 12) link_NAG-ASN : angle 2.22696 / 1.86 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3250.86 seconds wall clock time: 57 minutes 5.02 seconds (3425.02 seconds total)